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formula

InSilicoSpectro

view release on metacpan or search on metacpan

cgi/cgiInSilicoDef.pl view on Meta::CPAN

                </table>
              </td>
            </tr>
            <tr id="cleavsite_regexp">
              <td valign='top'>Regular expression</td>
              <td valign='top'><input type="radio" name="sitetype"  value="regexp" onclick="selectCleavSiteMode('regexp');"/></td>
              <td><input type='textfield' name='siteregexp'/></td>
            </tr>
          </table>

          <h5>Gain (formula)</h5>
          <table border=1 cellspacing=0>
            <tr>
              <td>N-term</td>
              <td><input type="textfield" name="NTermGain"/></td>
            </tr>
            <tr>
              <td>C-term</td>
              <td><input type="textfield" name="CTermGain"/></td>
            </tr>
          </table>

cgi/cgiInSilicoDef.pl view on Meta::CPAN

      print "    defList['$key']['cterm']=".($els->first_child("cterm")?'1':'0').";\n";
    } elsif($_->first_child('siteRegexp')){
      print "    defList['$key']['siteRegexp']='".$_->first_child('siteRegexp')->text."';\n";
      print "    defList['$key']['nterm']=".(0+$_->atts->{nterm}).";\n";
      print "    defList['$key']['cterm']=".(0+$_->atts->{cterm}).";\n";
    }else{#oldfashion
      print "    defList['$key']['residue']='".$_->first_child('residue')->atts->{a}."';\n";
    }
    print "    defList['$key']['delta_mono']='".$_->first_child('delta')->atts->{monoisotopic}."';\n";
    print "    defList['$key']['delta_avg']='".$_->first_child('delta')->atts->{average}."';\n";
    print "    defList['$key']['formula']='".($_->first_child('formula')?$_->first_child('formula')->text:'')."';\n";
    my $spft=($_->first_child('sprotFT'))?($_->first_child('sprotFT')->text):"";
    print "    defList['$key']['sprotFT']=\"$spft\";\n";
  }
  print <<EOT;

    function id2modresForm(id){
      document.define.key.value=id;
      document.test.key.value=id;

      document.define.key.disabled=1;

cgi/cgiInSilicoDef.pl view on Meta::CPAN

        document.define.residue.value=mr['residue'];
      }else{
        selectSiteMode('regexp');
        document.define.sitetype[1].checked=1;
        document.define.siteregexp.value=mr['siteRegexp'];
      }
      document.define.nterm.checked=mr['nterm'];
      document.define.cterm.checked=mr['cterm'];
      document.define.delta_mono.value=mr['delta_mono'];
      document.define.delta_avg.value=mr['delta_avg'];
      document.define.formula.value=mr['formula'];
      document.define.sprotFT.value=mr['sprotFT'];

    }

    function selectSiteMode(val){
      if(val == 'classic'){
        document.getElementById('site_regexp').bgColor='lightgrey';
        document.getElementById('site_classic').bgColor='white';
        document.define.sitetype[0].checked=1;
        document.define.residue.disabled=0;

cgi/cgiInSilicoDef.pl view on Meta::CPAN

              <td>mono isotopic</td>
              <td><input type="textfield" name="delta_mono"/></td>
            </tr>
            <tr>
              <td>average</td>
              <td><input type="textfield" name="delta_avg"/></td>
            </tr>
          </table>

          <h5>Formula</h5>
          <input type="textfield" name="formula"/>

          <hr width="100%"/>
          <center><h4>Uniprot annotations</h4></center>
          <h5>Uniprot FT mask</h5>
          <input type='textfield' size=80 name='sprotFT'/>
        </td>
      </tr>
      <tr>
EOT
  if ($edit){

cgi/cgiInSilicoDef.pl view on Meta::CPAN

    $contents.="<nterm/>" if $q->param('nterm');
    $contents.="<cterm/>" if $q->param('cterm');
    $contents.="</site>";
    my $els=XML::Twig::Elt->new()->parse($contents)->paste(last_child=>$el);;
  }else{
    my $atts;
    $atts.=" nterm='yes'" if $q->param('nterm');
    $atts.=" cterm='yes'" if $q->param('cterm');
    my $els=XML::Twig::Elt->new()->parse("<siteRegexp$atts><![CDATA[".$q->param('siteregexp')."]]></siteRegexp>")->paste(first_child=>$el);
  }
  my $formula=$q->param('formula');
  my $dm_mono=$q->param('delta_mono')||-999;
  my $dm_avg=$q->param('delta_avg')||-999;
  if ($formula){
    ($dm_mono, $dm_avg)=InSilicoSpectro::InSilico::MassCalculator::massFromComposition($formula);
  }
  XML::Twig::Elt->new()->parse("<delta monoisotopic='$dm_mono' average='$dm_avg'/>")->paste(last_child=>$el);
  XML::Twig::Elt->new()->parse("<formula>$formula</formula>")->paste(last_child=>$el) if $q->param('formula');
  XML::Twig::Elt->new()->parse("<sprotFT><![CDATA[".$q->param('sprotFT')."]]></sprotFT>")->paste(last_child=>$el);
}

lib/InSilicoSpectro/InSilico/IsoelPoint.pm view on Meta::CPAN

  foreach (keys %h) { $this->set($_, $h{$_}) }

  my $method=$this->{method};

  return $this->$method;
}


sub Patrickios {
# Isoelectric point prediction
# Patrickios' formula

  my ($this,%h)=@_;
  foreach (keys %h) { $this->set($_, $h{$_}) }

  my $pKa=$this->{pK}{Patrickios}{pKa};
  my $pKb=$this->{pK}{Patrickios}{pKb};
  my $A=1; # Carboxyl
  my $B=1; # Amino

  foreach (split '',$this->{peptide}) {

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN

  $isInit = 1;

} # init


# -----------------------------------------------------------------------------
# Gets and sets masses
# -----------------------------------------------------------------------------


=head2 massFromComposition($formula)

Computes monoisotopic and average masses from an atomic composition given
in $formula. Monoisotopic and average masses are returned as a vector of 2
elements. Negative numbers are possible to accommodate with losses or certain
modifications.

Example:

  print join(',', massFromComposition('HPO3')), "\n";

=cut
sub massFromComposition
{
  my ($formula) = @_;

  my $mono = 0;
  my $avg = 0;
  $formula =~ s/\s+//g;
  while ($formula =~ /([A-Z][a-z\+]?)([\-\d]*)/g){
    my $num = $2 || 1;
    $mono += $num*$elMass{"el_$1"}[0];
    $avg += $num*$elMass{"el_$1"}[1];
  }

  return ($mono, $avg);

} # massFromComposition

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN

  # Returns the mass of the given element/molecule, according to $massType or to the second argument if defined
  my ($el, $mt) = @_;

  $mt = $massType if(!defined($mt));
   defined($elMass{$el}) || ( $invalidElementCall && $invalidElementCall->("Unknown element/molecule in getMass: [$el]"));
  $elMass{$el}[$mt];

} # getMass


=head2 setMass($symbol, $formula)

This function allows the user to set new molecule, element, amino acid, and modification
masses dynamically.

=over 4

=item $symbol

Contains the identifier of the new object with the appropriate prefix (el_, aa_,
mol_, or mod_).

=item $formula

Contains the atomic composition (it is used for computing monoisotopic and average
masses). Negative numbers of atoms are possible to deal with modifications.

Examples:

setMass('mol_NH3', 'NH3');

setMass('mol_H2O', 'H2O');

=back

=cut
sub setMass
{
  my ($symbol, $formula) = @_;
  croak("Already defined mass for [$symbol]") if (defined($elMass{$symbol}));

  my ($mono, $avg) = massFromComposition($formula);
  $elMass{$symbol} = [$mono, $avg];

} # setMass


=head2 setMassType($type)

Sets the current mass type. C<$type> must be equal to 0 (monoisotopic) or 1 (average).

=cut

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN

  $dibasicRegex = qr/(?<=[KR])(?=[KR])/,

which is exported by this module.

When you specify the enzyme by a CleavEnzyme object, the regular expression is
read from the object.

=item CTermGain, NTermGain

In case the enzyme does not add H at N-termini and OH at C-termini, you can
define new formulas for what is added.

When the enzyme comes as a CleavEnzyme object, these values are read from the
enzyme object directly.

=item CTermModif, NTermModif

In case the enzyme does introduce a modification at peptide C-/N-termini, you can
provide the name of the modification to apply.

When the enzyme comes as a CleavEnzyme object, these values are read from the

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN

=cut
sub getSeries
{
  my ($name) = @_;

  return ($series{$name}{terminus}, $series{$name}{delta}[0], $series{$name}{delta}[1], $series{$name}{firstFrag}, $series{$name}{lastFrag});

} # getSeries


=head2 setSeries($name, $terminus, $formula, $firstFrag, $lastFrag)

Adds a new series to the series read from the configuration file.
The parameters are defined above in getSeries except formula.
The mass deltas are not given as real numbers but rather as
deltas in atoms. For instance, b series formula is empty because
we do want 0 delta and c series formula is 'N 1 H 3'. Example:

  setSeries('c', 'N', 'N 1 H 3', 2, 2);

=cut
sub setSeries
{
  my ($name, $terminus, $formula, $firstFrag, $lastFrag) = @_;
  croak("Already defined series for [$name]") if (defined($series{$name}));

  $series{$name}{terminus} = uc($terminus);
  $series{$name}{delta} = [massFromComposition($formula)];
  $series{$name}{firstFrag} = $firstFrag;
  $series{$name}{lastFrag} = $lastFrag;

} # setSeries


=head2 getLoss($name)

Returns a vector (residues, monoisotopic delta, average delta)
that contains the parameters of a neutral loss, where

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN

=cut
sub getLoss
{
  my ($name) = @_;

  return (join('', keys(%{$loss{$name}{residues}})), $loss{$name}{delta}[0], $loss{$name}{delta}[1]);

} # getLoss


=head2 setLoss($name, $residues, $formula)
=head2 setLoss($name, $residues, $deltamass_mono, $deltamass_avg)

Adds a new loss to the ones read from the file fragments.xml.
The parameters are defined above in getLoss except formula.
The mass deltas are not given as real numbers but rather as
deltas in atoms. Example:

  setLoss('H2O', 'ST', 'H 2 O 1');
or 
  setLoss('H2O', 'ST', 18.003, 17.927);

=cut
sub setLoss
{
  my $name=shift;
  my $residues=shift;
  if($_[0]=~/^[A-Z]/){
    #we have a formula
    my $formula=shift;
    croak("Already defined loss for [$name]") if (defined($loss{$name}));
    $loss{$name}{delta} = [massFromComposition($formula)];
  }else{
    # we should have two masses
    $loss{$name}{delta} = [$_[0], $_[1]];
  }

  foreach (split(//, $residues)){
    $loss{$name}{residues}{$_} = 1;
  }

} # setLoss

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN

  my ($twig, $el) = @_;

  my $symbol = $el->atts->{symbol};
  my ($mono, $avg);
  if (my $mel = $el->first_child('mass')){
    # Mass directly provided, use it
    $mono = $mel->atts->{monoisotopic};
    $avg = $mel->atts->{average};
  }
  else{
    # Use the formula instead
    my $formula = $el->first_child('formula')->text;
    ($mono, $avg) = massFromComposition($formula);
  }
  $elMass{"mol_$symbol"} = [$mono, $avg];

} # twigAddMolecule


sub twigAddAminoAcid
{
  my ($twig, $el) = @_;
  my $symbol = $el->atts->{code1};

lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN



sub twigAddSeries
{
  my ($twig, $el) = @_;

  my $name = $el->atts->{name};
  my $terminus = $el->first_child('terminus')->text;
  my $firstFrag = $el->first_child('firstFragment')->text;
  my $lastFrag = $el->first_child('lastFragment')->text;
  my $formula = $el->first_child('formula')->text;
  setSeries($name, $terminus, $formula, $firstFrag, $lastFrag);

} # twigAddSeries


sub twigAddLoss
{
  my ($twig, $el) = @_;

  my $name = $el->atts->{name};
  my $residues = $el->first_child('residues')->atts->{aa};
  my $formula = $el->first_child('formula')&&$el->first_child('formula')->text;
  if($formula){
    setLoss($name, $residues, $formula);
  }else{
    my $eldm=$el->first_child('deltaMass')|| die "must specify 'formula' or 'deltamass' in oneLoss definition [$name]";
    $eldm->print(\*STDERR);
    setLoss($name, $residues, $eldm->atts->{monoisotopic}, $eldm->atts->{average});
  }

} # twigAddLoss


sub twigAddFragType
{
  my ($twig, $el) = @_;

lib/InSilicoSpectro/InSilico/ModRes.pm view on Meta::CPAN

    $termtag.='<cterm/>' if($this->cTerm);
    XML::Twig::Elt->new()->parse("<site><residue>$this->{site}{residue}</residue>$termtag</site>")->paste(last_child=>$el);
  }else{
    my $termatts="";
    $termatts=' nterm="yes"' if($this->nTerm);
    $termatts=' cterm="yes"' if($this->cTerm);
    XML::Twig::Elt->new()->parse("<siteRegexp$termatts>$this->{regexpStr}</siteRegexp>")->paste(last_child=>$el);
  }
  XML::Twig::Elt->new()->parse("<delta monoisotopic='$this->{delta_monoisotopic}' average='$this->{delta_average}'/>")->paste(last_child=>$el);

  XML::Twig::Elt->new()->parse("<formula>$this->{formula}</formula>")->paste(last_child=>$el);
  XML::Twig::Elt->new()->parse("<sprotFT><![CDATA[$this->{sprotFT}]]></sprotFT>")->paste(last_child=>$el) if $this->{sprotFT};
  return $el;
}

sub registerModResHandler{
  my $sub=shift;
  if($sub){
    $rsRegisterModResHandler=$sub;
  }
  return $rsRegisterModResHandler;

lib/InSilicoSpectro/config/RESID.insilicodef.xml view on Meta::CPAN

<inSilicoDefinitions>
  <elements/>
  <aminoAcids/>
  <codons/>
  <cleavEnzymes>
  </cleavEnzymes>
  <fragTypeDescriptions/>
  <modRes>
<oneModRes name="(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5p-adenosine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="386.30" monoisotopic="386.1103"/><formula>C13H19N6O6P1</formula><sprotFT><![CDATA[...
<oneModRes name="(E)-2,3-didehydrotyrosine" type="aaModif"><description>Crystal structure of coral pigment.</description><site><residue>Y</residue></site><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0</formula><sprotFT><![CDATA[(No...
<oneModRes name="(Z)-2,3-didehydrotyrosine" type="aaModif"><description>Structure of green fluorescent protein.</description><site><residue>Y</residue></site><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0</formula><sprotFT><![CDATA...
<oneModRes name="(Z)-dehydrobutyrine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Modified site: (Z)-dehydrobutyrine (Thr)...
<oneModRes name="(phospho-5p-guanosine)-L-histidine" type="aaModif"><description>The three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced...
<oneModRes name="1-chondroitin sulfate-L-aspartic acid ester" type="aaModif"><description></description><site><residue>D</residue></site><delta average="441.36 +" monoisotopic="441.0576 +"/><formula>C14H19N1O13S1+</formula><sprotFT><![CDATA[(Modified...
<oneModRes name="1-thioglycine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="16.06" monoisotopic="15.9772"/><formula>C0H0N0O-1S1</formula><sprotFT><![CDATA[(Modified site: 1-thioglycine (Gly)|Modified sit...
<oneModRes name="1p-(8alpha-FAD)-L-histidine" type="aaModif"><description>Structure of the octameric flavoenzyme vanillyl-alcohol oxidase.</description><site><residue>H</residue></site><delta average="783.53" monoisotopic="783.1414"/><formula>C27H31N...
<oneModRes name="1p-(8alpha-FMN)-L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="454.33" monoisotopic="454.0889"/><formula>C17H19N4O9P1</formula><sprotFT><![CDATA[(Modified site: 3'-FAD-histidin...
<oneModRes name="1p-(phospho-5p-adenosine)-L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="329.21" monoisotopic="329.0525"/><formula>C10H12N5O6P1</formula><sprotFT><![CDATA[(Not available|ACT_SI...
<oneModRes name="1p-(phospho-5p-uridine)-L-histidine" type="aaModif"><description>The structure of nucleotidylated galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.86 Angstroms resolution.</description><site><residue>H</residue></...
<oneModRes name="1p-glycosyl-L-tryptophan" type="aaModif"><description></description><site><residue>W</residue></site><delta average="0.00 +" monoisotopic="0.0000 +"/><formula>C0H0N0O0+</formula><sprotFT><![CDATA[(Binding site: carbohydrate (Trp) (co...
<oneModRes name="1p-heme-L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="616.49" monoisotopic="616.1773"/><formula>C34Fe1H32N4O4</formula><sprotFT><![CDATA[(Not available|BINDING Heme (covalent)...
<oneModRes name="1p-methyl-L-histidine" type="aaModif"><description>Uncomplexed actin.</description><site><residue>H</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES Me...
<oneModRes name="1p-phospho-L-histidine" type="aaModif"><description>E. coli cofactor-dependent phosphoglycerate mutase.</description><site><residue>H</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotF...
<oneModRes name="2-(S-L-cysteinyl)-D-allo-threonine" type="aaModif"><description></description><siteRegexp>C.*?T</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0</formula><sprotFT><![CDATA[(Cross-link: 2-cysteinyl-D-all...
<oneModRes name="2-(S-L-cysteinyl)-D-phenylalanine" type="aaModif"><description></description><siteRegexp>C.*?F</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0</formula><sprotFT><![CDATA[(Cross-link: 2-cysteinyl-D-phen...
<oneModRes name="2-(S-L-cysteinyl)-L-phenylalanine" type="aaModif"><description></description><siteRegexp>C.*?F</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0</formula><sprotFT><![CDATA[(Cross-link: 2-cysteinyl-L-phen...
<oneModRes name="2-imino-glutamic acid 5-imidazolinone glycine" type="aaModif"><description></description><siteRegexp>E.*?G</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1</formula><sprotFT><![CDATA[(Not available|CRO...
<oneModRes name="2-imino-glutamine 5-imidazolinone glycine" type="aaModif"><description>Crystal structure of DsRed, a red fluorescent protein from Discosoma sp. red.</description><siteRegexp>G.*?Q</siteRegexp><delta average="-20.03" monoisotopic="-20...
<oneModRes name="2-imino-methionine 5-imidazolinone glycine" type="aaModif"><description>Variations on the GFP chromophore: A fragmented 5-membered heterocycle revealed in the 2.1A crystal structure of a non-fluorescent chromoprotein.</description><s...
<oneModRes name="2-methyl-L-glutamine" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: 2-methylglutamine (Gln)|MOD_...
<oneModRes name="2-oxobutanoic acid" type="aaModif"><description></description><site><residue>T</residue></site><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0</formula><sprotFT><![CDATA[(Modified site: 2-oxobutanoic acid (Thr) (...
<oneModRes name="2-pyrrolidone-5-carboxylic acid" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0</formula><sprotFT><![CDATA[(Modified site: pyrrolidone c...
<oneModRes name="2-tetrahydropyridinyl-5-imidazolinone glycine" type="aaModif"><description>Crystal Structure of Wild Type Yellow Fluorescent Protein zFP538 from Zoanthus.</description><siteRegexp>G.*?K</siteRegexp><delta average="-37.06" monoisotopi...
<oneModRes name="2p-(S-L-cysteinyl)-L-histidine" type="aaModif"><description></description><siteRegexp>C.*?H</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0</formula><sprotFT><![CDATA[(Cross-link: cysteinylhistidine (C...
<oneModRes name="2p-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine" type="aaModif"><description>Crystal structure of ADP-ribosylated ribosomal translocase from Saccharomyces cerevisiae.</description><site><residue>H</residue></site><delta ave...
<oneModRes name="2p-alpha-mannosyl-L-tryptophan" type="aaModif"><description></description><site><residue>W</residue></site><delta average="162.14" monoisotopic="162.0528"/><formula>C6H10N0O5</formula><sprotFT><![CDATA[(Modified site: 2'-mannosyl-try...
<oneModRes name="3,4-dihydroxy-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="32.00" monoisotopic="31.9898"/><formula>C0H0N0O2</formula><sprotFT><![CDATA[(Not available|MOD_RES 3,4-dihydroxyargi...
<oneModRes name="3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one" type="aaModif"><description></description><siteRegexp>M.*?Y</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><...
<oneModRes name="3-(3p-L-histidyl)-L-tyrosine" type="aaModif"><description></description><siteRegexp>H.*?Y</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0</formula><sprotFT><![CDATA[(Cross-link: 3'-histidyl-3-tyrosine (H...
<oneModRes name="3-(S-L-cysteinyl)-L-aspartic acid" type="aaModif"><description>Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking.</description><siteRegexp>C.*?D</siteRegexp><delta averag...
<oneModRes name="3-hydroxy-L-proline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: 3-hydroxyproline (Pro)|MOD_RE...
<oneModRes name="3-hydroxy-L-tryptophan" type="aaModif"><description>Lignin peroxidase (isozyme H2) pI=4.15.</description><site><residue>W</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(No...
<oneModRes name="3-methyl-L-lanthionine" type="aaModif"><description></description><siteRegexp>C.*?T</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: (2S,3S,6R)-3-methyl-lanthi...
<oneModRes name="3-methyl-L-lanthionine sulfoxide" type="aaModif"><description>NMR structure of the lantibiotic actagardine, 15 structures.</description><siteRegexp>C.*?T</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0...
<oneModRes name="3p,3pp,5p-triiodo-L-thyronine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="469.78" monoisotopic="469.7158"/><formula>C6H1I3N0O1</formula><sprotFT><![CDATA[(Modified site: triiodothyronin...
<oneModRes name="3p-(1p-L-histidyl)-L-tyrosine" type="aaModif"><description></description><siteRegexp>H.*?Y</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0</formula><sprotFT><![CDATA[(Cross-link: 1'-histidyl-3'-tyrosine ...
<oneModRes name="3p-(3p-L-tyrosinyl)-L-tyrosine" type="aaModif"><description></description><siteRegexp>Y.*?Y</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></...
<oneModRes name="3p-(8alpha-FAD)-L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="783.53" monoisotopic="783.1414"/><formula>C27H31N9O15P2</formula><sprotFT><![CDATA[(Modified site: 3'-FAD-histidi...
<oneModRes name="3p-(8alpha-FMN)-L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="454.33" monoisotopic="454.0889"/><formula>C17H19N4O9P1</formula><sprotFT><![CDATA[(Not available|MOD_RES Pros-8al...
<oneModRes name="3p-(O4p-L-tyrosinyl)-L-tyrosine" type="aaModif"><description>Crystallographic structure of Mycobacterium tuberculosis hemoglobin O.</description><siteRegexp>Y.*?Y</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0...
<oneModRes name="3p-(S-L-cysteinyl)-L-tyrosine" type="aaModif"><description>Structure of Mycobacterium tuberculosis NirA protein.</description><siteRegexp>C.*?Y</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0</formula>...
<oneModRes name="3p-heme-L-histidine" type="aaModif"><description>Solution structure of the heme chaperone CcmE of Escherichia coli.</description><site><residue>H</residue></site><delta average="616.49" monoisotopic="616.1773"/><formula>C34Fe1H32N4O4...
<oneModRes name="3p-methyl-L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: 3'-methylhistidine (His)|MO...
<oneModRes name="3p-phospho-L-histidine" type="aaModif"><description>Nucleoside diphosphate kinase (E.C. 2.7.4.6).</description><site><residue>H</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotFT><![C...
<oneModRes name="4,5-dihydroxy-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="32.00" monoisotopic="31.9898"/><formula>C0H0N0O2</formula><sprotFT><![CDATA[(Not available|MOD_RES 4,5-dihydroxylysine...
<oneModRes name="4-(S-L-cysteinyl)-L-glutamic acid" type="aaModif"><description>Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking.</description><siteRegexp>C.*?E</siteRegexp><delta averag...
<oneModRes name="4-amino-3-isothiazolidinone-L-serine" type="aaModif"><description>Oxidation state of protein tyrosine phosphatase 1B.</description><siteRegexp>C.*?S</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0</for...
<oneModRes name="4-hydroxy-L-arginine" type="aaModif"><description>Carbon monoxide dehydrogenase from Hydrogenophaga pseudoflava.</description><site><residue>R</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula>...
<oneModRes name="4-hydroxy-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: 4-hydroxylysine (Lys)|Not avai...
<oneModRes name="4-hydroxy-L-proline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: 4-hydroxyproline (Pro)|MOD_RE...
<oneModRes name="4p-(L-tryptophan)-L-tryptophyl quinone" type="aaModif"><description></description><siteRegexp>W.*?W</siteRegexp><delta average="27.97" monoisotopic="27.9585"/><formula>C0H-4N0O2</formula><sprotFT><![CDATA[(Cross-link: tryptophan-tryp...
<oneModRes name="4p-(S-L-cysteinyl)-L-tryptophyl quinone" type="aaModif"><description>Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking.</description><siteRegexp>C.*?W</siteRegexp><delta ...
<oneModRes name="5-hydroxy-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: 5-hydroxylysine (Lys)|MOD_RES ...
<oneModRes name="5-hydroxy-N6,N6,N6-trimethyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="59.09" monoisotopic="59.0497"/><formula>C3H7N0O1</formula><sprotFT><![CDATA[(Not available|MOD_RES N6,N...
<oneModRes name="5-methyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: 5-methylarginine (Arg)|MOD_RE...
<oneModRes name="5p-(N6-L-lysine)-L-topaquinone" type="aaModif"><description></description><siteRegexp>K.*?Y</siteRegexp><delta average="11.97" monoisotopic="11.9636"/><formula>C0H-4N0O1</formula><sprotFT><![CDATA[(Cross-link: lysine-topaquinone (Lys...
<oneModRes name="D-alanine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-16.00" monoisotopic="-15.9949"/><formula>C0H0N0O-1</formula><sprotFT><![CDATA[(Modified site: D-alanine (Ala)|Modified site: D-ala...
<oneModRes name="D-allo-isoleucine" type="aaModif"><description></description><site><residue>I</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0</formula><sprotFT><![CDATA[(Modified site: D-allo-isoleucine (Ile)|MOD_RES D...
<oneModRes name="D-asparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0</formula><sprotFT><![CDATA[(Modified site: D-asparagine (Asn)|MOD_RES D-asparagin...
<oneModRes name="D-leucine" type="aaModif"><description></description><site><residue>L</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0</formula><sprotFT><![CDATA[(Modified site: D-leucine (Leu)|MOD_RES D-leucine).*]]></...
<oneModRes name="D-methionine" type="aaModif"><description></description><site><residue>M</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0S0</formula><sprotFT><![CDATA[(Modified site: D-methionine (Met)|MOD_RES D-methion...
<oneModRes name="D-phenylalanine" type="aaModif"><description></description><site><residue>F</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0</formula><sprotFT><![CDATA[(Modified site: D-phenylalanine (Phe)|MOD_RES D-phe...
<oneModRes name="D-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0</formula><sprotFT><![CDATA[(Modified site: D-serine (Ser)|MOD_RES D-serine).*]]></spr...
<oneModRes name="D-tryptophan" type="aaModif"><description></description><site><residue>W</residue></site><delta average="0.00" monoisotopic="0.0000"/><formula>C0H0N0O0</formula><sprotFT><![CDATA[(Modified site: D-tryptophan (Trp)|MOD_RES D-tryptopha...
<oneModRes name="L-2-aminoadipic acid" type="aaModif"><description></description><site><residue>K</residue></site><delta average="14.97" monoisotopic="14.9633"/><formula>C0H-3N-1O2</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotF...
<oneModRes name="L-2p,4p,5p-topaquinone" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="29.98" monoisotopic="29.9742"/><formula>C0H-2N0O2</formula><sprotFT><![CDATA[(Modified site: topaquinone (Tyr)|MOD_RES...
<oneModRes name="L-2p-bromophenylalanine" type="aaModif"><description></description><site><residue>F</residue></site><delta average="78.90" monoisotopic="77.9105"/><formula>Br1C0H-1N0O0</formula><sprotFT><![CDATA[(Modified site: 2'-bromophenylalanine...
<oneModRes name="L-3-oxoalanine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0</formula><sprotFT><![CDATA[(Modified site: 3-oxoalanine (Cys)|Modified site:...
<oneModRes name="L-3-phenyllactic acid" type="aaModif"><description></description><site><residue>F</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Modified site: L-3-phenyllactic acid (Phe)...
<oneModRes name="L-3p,4p,5p-trihydroxyphenylalanine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="32.00" monoisotopic="31.9898"/><formula>C0H0N0O2</formula><sprotFT><![CDATA[(Modified site: 3',4',5'-trihy...
<oneModRes name="L-3p,4p-dihydroxyphenylalanine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: 3',4'-dihydroxyphe...
<oneModRes name="L-3p-bromophenylalanine" type="aaModif"><description></description><site><residue>F</residue></site><delta average="78.90" monoisotopic="77.9105"/><formula>Br1C0H-1N0O0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></s...
<oneModRes name="L-4p-bromophenylalanine" type="aaModif"><description></description><site><residue>F</residue></site><delta average="78.90" monoisotopic="77.9105"/><formula>Br1C0H-1N0O0</formula><sprotFT><![CDATA[(Modified site: 4'-bromophenylalanine...
<oneModRes name="L-6p-bromotryptophan" type="aaModif"><description></description><site><residue>W</residue></site><delta average="78.90" monoisotopic="77.9105"/><formula>Br1C0H-1N0O0</formula><sprotFT><![CDATA[(Modified site: 6-bromotryptophan (Trp)|...
<oneModRes name="L-alanine" type="aaModif"><description></description><site><residue>A</residue></site><delta average="" monoisotopic=""/><formula></formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></oneModRes>
<oneModRes name="L-alanine 5-imidazolinone glycine" type="aaModif"><description></description><siteRegexp>A.*?G</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Cross-link: 5-imidazolinone (...
<oneModRes name="L-alanine amide" type="aaModif"><description></description><site><residue>A</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Ala)|Modi...
<oneModRes name="L-alanyl-pentaglycyl-murein peptidoglycan" type="aaModif"><description></description><site><residue>A</residue></site><delta average="268.25 +" monoisotopic="268.1045 +"/><formula>C10H14N5O4+</formula><sprotFT><![CDATA[(Not available...
<oneModRes name="L-allysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="-1.03" monoisotopic="-1.0316"/><formula>C0H-3N-1O1</formula><sprotFT><![CDATA[(Modified site: allysine (Lys)|MOD_RES Allysine).*]]...
<oneModRes name="L-alpha-aminoacid" type="aaModif"><description></description><site><residue>X</residue></site><delta average="" monoisotopic=""/><formula></formula><sprotFT><![CDATA[().*]]></sprotFT></oneModRes>
<oneModRes name="L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="" monoisotopic=""/><formula></formula><sprotFT><![CDATA[(Active site: Arg|ACT_SITE).*]]></sprotFT></oneModRes>
<oneModRes name="L-arginine amide" type="aaModif"><description></description><site><residue>R</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Arg)|Mod...
<oneModRes name="L-asparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="" monoisotopic=""/><formula></formula><sprotFT><![CDATA[(Active site: Asn|ACT_SITE).*]]></sprotFT></oneModRes>
<oneModRes name="L-asparagine 5-imidazolinone glycine" type="aaModif"><description></description><siteRegexp>G.*?N</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Not available|CROSSLNK 5-i...
<oneModRes name="L-asparagine amide" type="aaModif"><description></description><site><residue>N</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Asn)|M...
<oneModRes name="L-aspartic 4-phosphoric anhydride" type="aaModif"><description></description><site><residue>D</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotFT><![CDATA[(Active site: Asp (aspartylph...
<oneModRes name="L-aspartic acid" type="aaModif"><description></description><site><residue>N</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Asp|Modified site: aspartic acid (A...
<oneModRes name="L-aspartic acid 1-amide" type="aaModif"><description></description><site><residue>D</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (A...
<oneModRes name="L-aspartic acid or L-asparagine" type="aaModif"><description></description><site><residue>B</residue></site><delta average="46.90" monoisotopic="47.9445"/><formula>C0H0N0O0S-1Se1</formula><sprotFT><![CDATA[().*]]></sprotFT></oneModRe...
<oneModRes name="L-aspartimide" type="aaModif"><description></description><site><residue>N</residue></site><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></o...
<oneModRes name="L-aspartyl aldehyde" type="aaModif"><description></description><site><residue>D</residue></site><delta average="-16.00" monoisotopic="-15.9949"/><formula>C0H0N0O-1</formula><sprotFT><![CDATA[(Not available|MOD_RES Aspartyl aldehyde)....
<oneModRes name="L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide)" type="aaModif"><description>Crystal structure of NarGH complex.</description><site><residue>D</residue></site><delta average="1572.01" monoisotopic="1571.0202"/><formula>...
<oneModRes name="L-beta-carboxyaspartic acid" type="aaModif"><description></description><site><residue>D</residue></site><delta average="44.01" monoisotopic="43.9898"/><formula>C1H0N0O2</formula><sprotFT><![CDATA[(Not available|Not available).*]]></s...
<oneModRes name="L-beta-methylthioasparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="46.09" monoisotopic="45.9877"/><formula>C1H2N0O0S1</formula><sprotFT><![CDATA[(Not available|Not available).*]]><...
<oneModRes name="L-beta-methylthioaspartic acid" type="aaModif"><description></description><site><residue>D</residue></site><delta average="46.09" monoisotopic="45.9877"/><formula>C1H2N0O0S1</formula><sprotFT><![CDATA[(Modified site: beta-methylthioa...
<oneModRes name="L-bromohistidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="78.90" monoisotopic="77.9105"/><formula>Br1C0H-1N0O0</formula><sprotFT><![CDATA[(Modified site: bromohistidine (His)|MOD_RES...
<oneModRes name="L-citrulline" type="aaModif"><description></description><site><residue>R</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Modified site: citrulline (Arg)|MOD_RES Citrulline)...
<oneModRes name="L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Cys|Active site: Cys (cysteine thiyl rad...
<oneModRes name="L-cysteine 5-imidazolinone glycine" type="aaModif"><description></description><siteRegexp>C.*?G</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: 5-imidazolinon...
<oneModRes name="L-cysteine amide" type="aaModif"><description></description><site><residue>C</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1S0</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Cys)|M...
<oneModRes name="L-cysteine coenzyme A disulfide" type="aaModif"><description></description><site><residue>C</residue></site><delta average="765.52" monoisotopic="765.0995"/><formula>C21H34N7O16P3S1</formula><sprotFT><![CDATA[(Not available|Not avail...
<oneModRes name="L-cysteine glutathione disulfide" type="aaModif"><description></description><site><residue>C</residue></site><delta average="305.31" monoisotopic="305.0681"/><formula>C10H15N3O6S1</formula><sprotFT><![CDATA[(Binding site: glutathione...
<oneModRes name="L-cysteine methyl disulfide" type="aaModif"><description>The NMR solution structure of the 3Fe ferredoxin II from Desulfovibrio gigas, 15 structures.</description><site><residue>C</residue></site><delta average="46.09" monoisotopic="...
<oneModRes name="L-cysteine methyl ester" type="aaModif"><description></description><site><residue>C</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0S0</formula><sprotFT><![CDATA[(Modified site: methyl ester carboxyl e...
<oneModRes name="L-cysteine oxazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?S</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: oxazole (Cys-Se...
<oneModRes name="L-cysteine oxazolinecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?S</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: 2-oxazoline (...
<oneModRes name="L-cysteine persulfide" type="aaModif"><description></description><site><residue>C</residue></site><delta average="32.06" monoisotopic="31.9721"/><formula>C0H0N0O0S1</formula><sprotFT><![CDATA[(Active site: Cys (cysteine persulfide in...
<oneModRes name="L-cysteine sulfenic acid" type="aaModif"><description></description><site><residue>C</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1S0</formula><sprotFT><![CDATA[(Active site: Cys (cysteine sulfenic a...
<oneModRes name="L-cysteine sulfinic acid" type="aaModif"><description></description><site><residue>C</residue></site><delta average="32.00" monoisotopic="31.9898"/><formula>C0H0N0O2S0</formula><sprotFT><![CDATA[(Modified site: cysteine sulfinic acid...
<oneModRes name="L-cysteine thiazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?C</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: thiazole (Cys-...
<oneModRes name="L-cysteinyl copper sulfido molybdopterin cytosine dinuncleotide" type="aaModif"><description>Crystal structure of the Cu,Mo-CO dehydrogenase (CODH); carbon monoxide reduced state.</description><site><residue>C</residue></site><delta ...
<oneModRes name="L-cysteinyl hydrogenase diiron subcluster" type="aaModif"><description>Fe-only hydrogenase from Clostridium pasteurianum.</description><site><residue>C</residue></site><delta average="342.87" monoisotopic="342.7869"/><formula>C5Fe2H-...
<oneModRes name="L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" type="aaModif"><description></description><site><residue>C</residue></site><delta average="1572.01" monoisotopic="1571.0202"/><formula>C40H47Mo1N20O26P4S4</formula><spro...
<oneModRes name="L-cysteinyl molybdopterin" type="aaModif"><description>The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals.</description><site><residue>C</residue></site><delta average="520.27...
<oneModRes name="L-cysteinyl-L-histidino-homocitryl molybdenum heptairon nitride nonasulfide" type="aaModif"><description>Nitrogenase MoFe protein from Azotobacter vinelandii.</description><siteRegexp>C.*?H</siteRegexp><delta average="991.56" monoiso...
<oneModRes name="L-cysteinyl-L-selenocysteine" type="aaModif"><description></description><siteRegexp>C.*?U</siteRegexp><delta average="-2.02" monoisotopic="-2.0156"/><formula>C0H-2N0O0S0Se0</formula><sprotFT><![CDATA[(Not available|CROSSLNK Cysteinyl...
<oneModRes name="L-cystine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="119.14" monoisotopic="119.0041"/><formula>C3H5N1O2S1</formula><sprotFT><![CDATA[(Disulfide bonds:|Disulfide bonds: interchain|Disul...
<oneModRes name="L-erythro-beta-hydroxyasparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: erythro-beta-hyd...
<oneModRes name="L-erythro-beta-hydroxyaspartic acid" type="aaModif"><description></description><site><residue>D</residue></site><delta average="16.00" monoisotopic="15.9949"/><formula>C0H0N0O1</formula><sprotFT><![CDATA[(Modified site: erythro-beta-...
<oneModRes name="L-gamma-carboxyglutamic acid" type="aaModif"><description></description><site><residue>E</residue></site><delta average="44.01" monoisotopic="43.9898"/><formula>C1H0N0O2</formula><sprotFT><![CDATA[(Modified site: gamma-carboxyglutami...
<oneModRes name="L-glutamic acid" type="aaModif"><description></description><site><residue>E</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Glu|ACT_SITE).*]]></sprotFT></oneMo...
<oneModRes name="L-glutamic acid 1-amide" type="aaModif"><description></description><site><residue>E</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (G...
<oneModRes name="L-glutamic acid 5-methyl ester" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="15.01" monoisotopic="14.9997"/><formula>C1H1N-1O1</formula><sprotFT><![CDATA[(Modified site: glutamate methyl ...
<oneModRes name="L-glutamic acid or L-glutamine" type="aaModif"><description></description><site><residue>Z</residue></site><delta average="46.90" monoisotopic="47.9445"/><formula>C0H0N0O0S-1Se1</formula><sprotFT><![CDATA[().*]]></sprotFT></oneModRes...
<oneModRes name="L-glutamimide" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></o...
<oneModRes name="L-glutamine" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Not available|ACT_SITE).*]]></sprotFT></oneModRes>
<oneModRes name="L-glutamine amide" type="aaModif"><description>[Pro7,13] alphaA-conotoxin PIVa, NMR, 12 structures.</description><site><residue>Q</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![...
<oneModRes name="L-glutamyl 5-glycerylphosphorylethanolamine" type="aaModif"><description></description><site><residue>E</residue></site><delta average="197.13" monoisotopic="197.0453"/><formula>C5H12N1O5P1</formula><sprotFT><![CDATA[(Binding site: g...
<oneModRes name="L-glutamyl 5-omega-hydroxyceramide ester" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="761.30 +" monoisotopic="760.7308 +"/><formula>C50H96N0O4+</formula><sprotFT><![CDATA[(Not available|...
<oneModRes name="L-glutamyl-5-poly(ADP-ribose)" type="aaModif"><description></description><site><residue>E</residue></site><delta average="541.30 +" monoisotopic="541.0610 +"/><formula>C15H21N5O13P2+</formula><sprotFT><![CDATA[(Not available|MOD_RES ...
<oneModRes name="L-histidine" type="aaModif"><description></description><site><residue>H</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: His|ACT_SITE).*]]></sprotFT></oneModRes...
<oneModRes name="L-histidine amide" type="aaModif"><description>Determination of the three-dimensional solution structure of scyllatoxin by 1H nuclear magnetic resonance.</description><site><residue>H</residue></site><delta average="-0.98" monoisotop...
<oneModRes name="L-isoglutamyl-polyglutamic acid" type="aaModif"><description></description><site><residue>E</residue></site><delta average="129.11 +" monoisotopic="129.0426 +"/><formula>C5H7N1O3+</formula><sprotFT><![CDATA[(Binding site: polyglutama...
<oneModRes name="L-isoglutamyl-polyglycine" type="aaModif"><description></description><site><residue>E</residue></site><delta average="57.05 +" monoisotopic="57.0215 +"/><formula>C2H3N1O1+</formula><sprotFT><![CDATA[(Binding site: polyglycine (Glu) (...
<oneModRes name="L-isoleucine" type="aaModif"><description></description><site><residue>I</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></oneMod...
<oneModRes name="L-isoleucine amide" type="aaModif"><description></description><site><residue>I</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Ile)|M...
<oneModRes name="L-isoleucine or L-leucine" type="aaModif"><description></description><site><residue>J</residue></site><delta average="663.14" monoisotopic="663.2214"/><formula>C0Fe8H-8N0O0S7</formula><sprotFT><![CDATA[().*]]></sprotFT></oneModRes>
<oneModRes name="L-lanthionine" type="aaModif"><description></description><siteRegexp>C.*?S</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1S0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></on...
<oneModRes name="L-leucine" type="aaModif"><description></description><site><residue>L</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></oneModRes...
<oneModRes name="L-leucine amide" type="aaModif"><description></description><site><residue>L</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Leu)|Modi...
<oneModRes name="L-leucine methyl ester" type="aaModif"><description></description><site><residue>L</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES Leucine methyl este...
<oneModRes name="L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Lys|ACT_SITE|ACT_SITE Schiff-base intermed...
<oneModRes name="L-lysine 5-imidazolinone glycine" type="aaModif"><description></description><siteRegexp>G.*?K</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Not available|CROSSLNK 5-imida...
<oneModRes name="L-lysine amide" type="aaModif"><description></description><site><residue>K</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Lys)|Modif...
<oneModRes name="L-lysine methyl ester" type="aaModif"><description></description><site><residue>K</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES Lysine methyl ester)...
<oneModRes name="L-lysine thiazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?K</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: thiazole (Lys-Cy...
<oneModRes name="L-lysinoalanine" type="aaModif"><description></description><siteRegexp>K.*?S</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Cross-link: (2Xi,9S)-lysinoalanine (Ser-Lys)|CR...
<oneModRes name="L-methionine" type="aaModif"><description></description><site><residue>M</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Met|Not available).*]]></sprotFT></one...
<oneModRes name="L-methionine amide" type="aaModif"><description></description><site><residue>M</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1S0</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Met)...
<oneModRes name="L-methionine sulfone" type="aaModif"><description></description><site><residue>M</residue></site><delta average="32.00" monoisotopic="31.9898"/><formula>C0H0N0O2S0</formula><sprotFT><![CDATA[(Modified site: methionine sulfone (Met)|M...
<oneModRes name="L-phenylalanine" type="aaModif"><description></description><site><residue>F</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Phe|Not available).*]]></sprotFT></...
<oneModRes name="L-phenylalanine amide" type="aaModif"><description>Crystal Structure of Wild Type Yellow Fluorescent Protein zFP538 from Zoanthus.</description><site><residue>F</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>...
<oneModRes name="L-phenylalanine thiazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?F</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: thiazole ...
<oneModRes name="L-proline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Pro|ACT_SITE Proton acceptor (via imino n...
<oneModRes name="L-proline amide" type="aaModif"><description></description><site><residue>P</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Pro)|Modi...
<oneModRes name="L-selenocysteine" type="aaModif"><description></description><site><residue>U</residue></site><delta average="46.90" monoisotopic="47.9445"/><formula>C0H0N0O0S-1Se1</formula><sprotFT><![CDATA[(Modified site: selenocysteine|SE_CYS).*]]...
<oneModRes name="L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)" type="aaModif"><description>Oxidized form of Formate Dehydrogenase H from E. coli.</description><site><residue>U</residue></site><delta average="1572.01" monoisoto...
<oneModRes name="L-selenocysteinyl tungsten bis(molybdopterin guanine dinucleotide)" type="aaModif"><description>Tungsten containing formate dehydrogenase from Desulfovibrio gigas.</description><site><residue>U</residue></site><delta average="1691.98...
<oneModRes name="L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Ser|ACT_SITE).*]]></sprotFT></oneModRes>
<oneModRes name="L-serine 5-imidazolinone glycine" type="aaModif"><description>Structure of green fluorescent protein.</description><siteRegexp>G.*?S</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><...
<oneModRes name="L-serine amide" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Ser)|Modif...
<oneModRes name="L-serine microcin E492 siderophore ester" type="aaModif"><description></description><site><residue>S</residue></site><delta average="831.69" monoisotopic="831.1969"/><formula>C36H37N3O20</formula><sprotFT><![CDATA[(Not available|MOD_...
<oneModRes name="L-serine thiazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?S</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: thiazole (Ser-Cy...
<oneModRes name="L-serinyl molybdenum bis(molybdopterin guanine dinucleotide)" type="aaModif"><description>The crystal structure of Rhodobacter sphaeroides dimethylsulfoxide reductase reveals two distinct molybdenum coordination environments.</descri...
<oneModRes name="L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Thr|ACT_SITE).*]]></sprotFT></oneModRes...
<oneModRes name="L-threonine amide" type="aaModif"><description></description><site><residue>T</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Thr)|Mo...
<oneModRes name="L-threonyl-pentaglycyl-murein peptidoglycan" type="aaModif"><description></description><site><residue>T</residue></site><delta average="268.25 +" monoisotopic="268.1045 +"/><formula>C10H14N5O4+</formula><sprotFT><![CDATA[(Not availab...
<oneModRes name="L-thyroxine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="595.68" monoisotopic="595.6123"/><formula>C6H0I4N0O1</formula><sprotFT><![CDATA[(Modified site: thyroxine (Tyr)|MOD_RES Thyroxine...
<oneModRes name="L-tryptophan" type="aaModif"><description></description><site><residue>W</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Trp|Active site: Trp (tryptophyl radic...
<oneModRes name="L-tryptophan amide" type="aaModif"><description></description><site><residue>W</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Trp)|M...
<oneModRes name="L-tryptophyl quinone" type="aaModif"><description></description><site><residue>W</residue></site><delta average="29.98" monoisotopic="29.9742"/><formula>C0H-2N0O2</formula><sprotFT><![CDATA[(Modified site: tryptophyl quinone (Trp)|MO...
<oneModRes name="L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Tyr|Active site: Tyr (stable tyrosyl rad...
<oneModRes name="L-tyrosine amide" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Tyr)|Mod...
<oneModRes name="L-valine" type="aaModif"><description></description><site><residue>V</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></oneModRes>
<oneModRes name="L-valine amide" type="aaModif"><description></description><site><residue>V</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Val)|Modif...
<oneModRes name="N,N,N-trimethyl-L-alanine" type="aaModif"><description></description><site><residue>A</residue></site><delta average="43.09" monoisotopic="43.0548"/><formula>C3H7N0O0</formula><sprotFT><![CDATA[(Modified site: trimethylated amino end...
<oneModRes name="N,N-dimethyl-L-proline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="29.06" monoisotopic="29.0391"/><formula>C2H5N0O0</formula><sprotFT><![CDATA[(Modified site: dimethylated amino end (Pr...
<oneModRes name="N-(L-glutamyl)-L-tyrosine" type="aaModif"><description></description><siteRegexp>E.*?Y</siteRegexp><delta average="-17.01" monoisotopic="-17.0027"/><formula>C0H-1N0O-1</formula><sprotFT><![CDATA[(Cross-link: peptide (Glu-Tyr) (by tub...
<oneModRes name="N-(L-isoaspartyl)-L-cysteine" type="aaModif"><description></description><siteRegexp>C.*?N</siteRegexp><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0S0</formula><sprotFT><![CDATA[(Cross-link: isopeptide amino end...
<oneModRes name="N-(L-isoaspartyl)-glycine" type="aaModif"><description></description><siteRegexp>G.*?N</siteRegexp><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0</formula><sprotFT><![CDATA[(Cross-link: isopeptide amino end (Gly...
<oneModRes name="N-(L-isoglutamyl)-glycine" type="aaModif"><description></description><siteRegexp>G.*?E</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Not available|CROSSLNK Isoglutamyl gl...
<oneModRes name="N-D-glucuronyl-glycine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="176.12" monoisotopic="176.0321"/><formula>C6H8N0O6</formula><sprotFT><![CDATA[(Modified site: glucuronylated amino end...
<oneModRes name="N-L-glutamyl-poly-L-glutamic acid" type="aaModif"><description></description><site><residue>E</residue></site><delta average="0.00 +" monoisotopic="0.0000 +"/><formula>C0H0N0O0+</formula><sprotFT><![CDATA[(Modified site: polyglutamat...
<oneModRes name="N-acetyl-L-alanine" type="aaModif"><description>Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution.</description><site><residue>A</re...
<oneModRes name="N-acetyl-L-aspartic acid" type="aaModif"><description>The structure of residues 7-16 of the Aalpha-chain of human fibrinogen bound to bovine thrombin at 2.3-A resolution.</description><site><residue>D</residue></site><delta average="...
<oneModRes name="N-acetyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1S0</formula><sprotFT><![CDATA[(Modified site: acetylated amino end (Cys)|...
<oneModRes name="N-acetyl-L-glutamic acid" type="aaModif"><description>Crystal structure of alpha1: implications for protein design.</description><site><residue>E</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formu...
<oneModRes name="N-acetyl-L-glutamine" type="aaModif"><description>Principles and pitfalls in designing site-directed peptide ligands.</description><site><residue>Q</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</for...
<oneModRes name="N-acetyl-L-isoleucine" type="aaModif"><description></description><site><residue>I</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formula><sprotFT><![CDATA[(Modified site: acetylated amino end (Ile)|...
<oneModRes name="N-acetyl-L-methionine" type="aaModif"><description></description><site><residue>M</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1S0</formula><sprotFT><![CDATA[(Modified site: acetylated amino end (Met...
<oneModRes name="N-acetyl-L-proline" type="aaModif"><description>Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains.</description><site><residue>P</residue></site><delta average="42.04" monoisotopic="42....
<oneModRes name="N-acetyl-L-serine" type="aaModif"><description>X-ray structure of a new crystal form of pike 4.10 beta parvalbumin.</description><site><residue>S</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formu...
<oneModRes name="N-acetyl-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formula><sprotFT><![CDATA[(Modified site: acetylated amino end (Thr)|M...
<oneModRes name="N-acetyl-L-tyrosine" type="aaModif"><description>Human P56-Lck tyrosine kinase SH2 Domain in complex with the phosphotyrosyl peptide Ac-PTyr-Glu-Glu-Ile (PYEEI peptide).</description><site><residue>Y</residue></site><delta average="4...
<oneModRes name="N-acetyl-L-valine" type="aaModif"><description></description><site><residue>V</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formula><sprotFT><![CDATA[(Modified site: acetylated amino end (Val)|Modi...
<oneModRes name="N-acetylglycine" type="aaModif"><description>High-resolution three-dimensional structure of horse heart cytochrome c.</description><site><residue>G</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</for...
<oneModRes name="N-alanyl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>A</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Modif...
<oneModRes name="N-asparaginyl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(...
<oneModRes name="N-aspartyl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>D</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Mod...
<oneModRes name="N-carbamoyl-L-alanine" type="aaModif"><description></description><site><residue>A</residue></site><delta average="43.02" monoisotopic="43.0058"/><formula>C1H1N1O1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT...
<oneModRes name="N-carboxy-L-methionine" type="aaModif"><description>Crystal structure LH2 B800-850 from Rps. acidophila at 2.0 angstrom resolution.</description><site><residue>M</residue></site><delta average="44.01" monoisotopic="43.9898"/><formula...
<oneModRes name="N-cysteinyl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1S0+</formula><sprotFT><![CDATA[(...
<oneModRes name="N-formyl-L-methionine" type="aaModif"><description></description><site><residue>M</residue></site><delta average="28.01" monoisotopic="27.9949"/><formula>C1H0N0O1S0</formula><sprotFT><![CDATA[(Modified site: N-formylmethionine|MOD_RE...
<oneModRes name="N-formyl-L-proline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="28.01" monoisotopic="27.9949"/><formula>C1H0N0O1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></...
<oneModRes name="N-formylglycine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="28.01" monoisotopic="27.9949"/><formula>C1H0N0O1</formula><sprotFT><![CDATA[(Modified site: formylated amino end (Gly) (in ma...
<oneModRes name="N-glycyl-1-(phosphatidyl)ethanolamine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="699.98 +" monoisotopic="699.5203 +"/><formula>C39H74N1O7P1+</formula><sprotFT><![CDATA[(Not available|L...
<oneModRes name="N-glycyl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Modif...
<oneModRes name="N-glycyl-glycosylsphingolipidinositolethanolamine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Not a...
<oneModRes name="N-methyl-L-alanine" type="aaModif"><description></description><site><residue>A</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: methylated amino end (Ala) (in...
<oneModRes name="N-methyl-L-isoleucine" type="aaModif"><description></description><site><residue>I</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES N-methylisoleucine)....
<oneModRes name="N-methyl-L-leucine" type="aaModif"><description></description><site><residue>L</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES N-methylleucine).*]]></...
<oneModRes name="N-methyl-L-methionine" type="aaModif"><description></description><site><residue>M</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0S0</formula><sprotFT><![CDATA[(Modified site: methylated amino end (Met...
<oneModRes name="N-methyl-L-phenylalanine" type="aaModif"><description></description><site><residue>F</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: methylated amino end (Ph...
<oneModRes name="N-methyl-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES N-methyltyrosine).*]]>...
<oneModRes name="N-methylglycine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: methylated amino end (Gly)|Modifi...
<oneModRes name="N-myristoyl-glycine" type="aaModif"><description>Ternary complex of a calcineurin A fragment, calcineurin B, Fkbp12 and the immunosuppressant drug FK506 (tacrolimus).</description><site><residue>G</residue></site><delta average="210....
<oneModRes name="N-palmitoyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="238.41 +" monoisotopic="238.2297 +"/><formula>C16H30N0O1S0+</formula><sprotFT><![CDATA[(Modified site: fatty acylated ...
<oneModRes name="N-palmitoyl-glycine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="238.41" monoisotopic="238.2297"/><formula>C16H30N0O1S0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></spr...
<oneModRes name="N-pyruvic acid 2-iminyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="70.05" monoisotopic="70.0055"/><formula>C3H2N0O2S0</formula><sprotFT><![CDATA[(Modified site: pyruvate 2-i...
<oneModRes name="N-pyruvic acid 2-iminyl-L-valine" type="aaModif"><description></description><site><residue>V</residue></site><delta average="70.05" monoisotopic="70.0055"/><formula>C3H2N0O2</formula><sprotFT><![CDATA[(Modified site: pyruvate 2-iminy...
<oneModRes name="N-seryl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Modifi...
<oneModRes name="N-seryl-glycosylsphingolipidinositolethanolamine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Modifi...
<oneModRes name="N-threonyl-glycosylphosphatidylinositolethanolamine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="123.05 +" monoisotopic="123.0085 +"/><formula>C2H6N1O3P1+</formula><sprotFT><![CDATA[(Not...
<oneModRes name="N2-acetyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formula><sprotFT><![CDATA[(Not available|MOD_RES N2-acetylarginine).*]...
<oneModRes name="N2-acetyl-L-lysine" type="aaModif"><description>NMR solution structure and flexibility of a peptide antigen representing the receptor binding domain of Pseudomonas aeruginosa.</description><site><residue>K</residue></site><delta aver...
<oneModRes name="N2-succinyl-L-tryptophan" type="aaModif"><description></description><site><residue>W</residue></site><delta average="100.07" monoisotopic="100.0160"/><formula>C4H4N0O3</formula><sprotFT><![CDATA[(Modified site: succinylated amino end...
<oneModRes name="N4,N4-dimethyl-L-asparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="28.05" monoisotopic="28.0313"/><formula>C2H4N0O0</formula><sprotFT><![CDATA[(Not available|MOD_RES N4,N4-dimethyl...
<oneModRes name="N4-(ADP-ribosyl)-L-asparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="541.30" monoisotopic="541.0610"/><formula>C15H21N5O13P2</formula><sprotFT><![CDATA[(Modified site: ADP-ribosyla...
<oneModRes name="N4-glycosyl-L-asparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="203.19 +" monoisotopic="203.0793 +"/><formula>C8H13N1O5+</formula><sprotFT><![CDATA[(Binding site: carbohydrate (Asn...
<oneModRes name="N4-hydroxymethyl-L-asparagine" type="aaModif"><description></description><site><residue>N</residue></site><delta average="30.03" monoisotopic="30.0106"/><formula>C1H2N0O1</formula><sprotFT><![CDATA[(Modified site: N4-hydroxymethylasp...
<oneModRes name="N4-methyl-L-asparagine" type="aaModif"><description>Structure of phycocyanin from Cyanidium caldarium at 1.65A resolution.</description><site><residue>N</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0...
<oneModRes name="N5-methyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT>...
<oneModRes name="N5-methyl-L-glutamine" type="aaModif"><description></description><site><residue>Q</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: N5-methylglutamine (Gln)|MO...
<oneModRes name="N6,N6,N6-trimethyl-L-lysine" type="aaModif"><description>Structure of the recombinant Paramecium tetraurelia calmodulin at 1.68 Angstrom resolution.</description><site><residue>K</residue></site><delta average="43.09" monoisotopic="4...
<oneModRes name="N6,N6-dimethyl-L-lysine" type="aaModif"><description>Structure of the recombinant Paramecium tetraurelia calmodulin at 1.68 Angstrom resolution.</description><site><residue>K</residue></site><delta average="28.05" monoisotopic="28.03...
<oneModRes name="N6-(4-amino-2-hydroxybutyl)-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="87.12" monoisotopic="87.0684"/><formula>C4H9N1O1</formula><sprotFT><![CDATA[(Modified site: N6-(4-amino-...
<oneModRes name="N6-(4-methyl-delta-1-pyrroline-5-carboxyl)-L-lysine" type="aaModif"><description>Crystal Structure of the Methanosarcina barkeri Monomethylamine Methyltransferase (MtmB).</description><site><residue>K</residue></site><delta average="...
<oneModRes name="N6-(L-isoaspartyl)-L-lysine" type="aaModif"><description></description><siteRegexp>K.*?N</siteRegexp><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0</formula><sprotFT><![CDATA[(Cross-link: isopeptide (Asn) (inter...
<oneModRes name="N6-(L-isoglutamyl)-L-lysine" type="aaModif"><description></description><siteRegexp>K.*?Q</siteRegexp><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0</formula><sprotFT><![CDATA[(Cross-link: isopeptide (Gln) (inter...
<oneModRes name="N6-(phospho-5p-adenosine)-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="329.21" monoisotopic="329.0525"/><formula>C10H12N5O6P1</formula><sprotFT><![CDATA[(Active site: Lys (coval...
<oneModRes name="N6-(phospho-5p-guanosine)-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="345.21" monoisotopic="345.0474"/><formula>C10H12N5O7P1</formula><sprotFT><![CDATA[(Active site: Lys (coval...
<oneModRes name="N6-1-carboxyethyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="72.06" monoisotopic="72.0211"/><formula>C3H4N0O2</formula><sprotFT><![CDATA[(Modified site: N6-1-carboxyethyllysin...
<oneModRes name="N6-3,4-didehydroretinylidene-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="264.41" monoisotopic="264.1878"/><formula>C20H24N0O0</formula><sprotFT><![CDATA[(Not available|Not avai...
<oneModRes name="N6-acetyl-L-lysine" type="aaModif"><description>2Fe-2S Ferredoxin from Haloarcula marismortui.</description><site><residue>K</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formula><sprotFT><![CDATA[...
<oneModRes name="N6-biotinyl-L-lysine" type="aaModif"><description>Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing.</description><site><residue>K</residue></site><delta average="226.29" monoisotopic="226.07...
<oneModRes name="N6-carboxy-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="44.01" monoisotopic="43.9898"/><formula>C1H0N0O2</formula><sprotFT><![CDATA[(Binding site: carbon dioxide (Lys) (covalent...
<oneModRes name="N6-formyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="28.01" monoisotopic="27.9949"/><formula>C1H0N0O1</formula><sprotFT><![CDATA[(Binding site: formyl (Lys) (covalent)|MOD_RES...
<oneModRes name="N6-glycyl-L-lysine" type="aaModif"><description></description><siteRegexp>G.*?K</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1</formula><sprotFT><![CDATA[(Cross-link: isopeptide carboxyl end (Gly) (i...
<oneModRes name="N6-lipoyl-L-lysine" type="aaModif"><description>H protein of the glycine cleavage system (aminomethyltransferase) (E.C.1.4.4.2).</description><site><residue>K</residue></site><delta average="188.31" monoisotopic="188.0330"/><formula>...
<oneModRes name="N6-methyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: N6-methyllysine (Lys)|MOD_RES ...
<oneModRes name="N6-mureinyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="-1.01 +" monoisotopic="-1.0078 +"/><formula>C0H-1N0O0+</formula><sprotFT><![CDATA[(Binding site: murein (Lys) (covalent)...
<oneModRes name="N6-myristoyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="210.36" monoisotopic="210.1984"/><formula>C14H26N0O1</formula><sprotFT><![CDATA[(Binding site: myristate (Lys) (covalen...
<oneModRes name="N6-palmitoyl-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="238.41" monoisotopic="238.2297"/><formula>C16H30N0O1</formula><sprotFT><![CDATA[(Binding site: palmitate (Lys) (covalen...
<oneModRes name="N6-propylamino-poly(propylmethylamino)-propyldimethylamine-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="426.73 +" monoisotopic="426.4410 +"/><formula>C24H54N6O0+</formula><sprot...
<oneModRes name="N6-pyridoxal phosphate-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="229.13" monoisotopic="229.0140"/><formula>C8H8N1O5P1</formula><sprotFT><![CDATA[(Binding site: pyridoxal phos...
<oneModRes name="N6-pyruvic acid 2-iminyl-L-lysine" type="aaModif"><description>N-Acetylneuraminate lyase in complex with hydroxypyruvate.</description><site><residue>K</residue></site><delta average="70.05" monoisotopic="70.0055"/><formula>C3H2N0O2<...
<oneModRes name="N6-retinylidene-L-lysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="266.42" monoisotopic="266.2034"/><formula>C20H26N0O0</formula><sprotFT><![CDATA[(Binding site: retinal (Lys) (covale...
<oneModRes name="O-(ADP-ribosyl)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="541.30" monoisotopic="541.0610"/><formula>C15H21N5O13P2</formula><sprotFT><![CDATA[(Modified site: ADP-ribosylserine...
<oneModRes name="O-(N-acetylglucosamine-1-phosphoryl)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="283.17" monoisotopic="283.0457"/><formula>C8H14N1O8P1</formula><sprotFT><![CDATA[(Not available...
<oneModRes name="O-(phospho-5p-DNA)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="78.97 +" monoisotopic="78.9585 +"/><formula>C0H0N0O3P1+</formula><sprotFT><![CDATA[(Binding site: phosphoryl-DNA ...
<oneModRes name="O-(phospho-5p-DNA)-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="78.97 +" monoisotopic="78.9585 +"/><formula>C0H0N0O3P1+</formula><sprotFT><![CDATA[(Binding site: phosphoryl-D...
<oneModRes name="O-(phospho-5p-RNA)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="78.97 +" monoisotopic="78.9585 +"/><formula>C0H0N0O3P1+</formula><sprotFT><![CDATA[(Binding site: phosphoryl-RNA ...
<oneModRes name="O-(phospho-5p-adenosine)-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="329.21" monoisotopic="329.0525"/><formula>C10H12N5O6P1</formula><sprotFT><![CDATA[(Binding site: AMP (Th...
<oneModRes name="O-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="242.12 +" monoisotopic="242.0191 +"/><formula>C6H11N0O8P1+</formula><sprotFT><![CDATA[(No...
<oneModRes name="O-(phosphoribosyl dephospho-coenzyme A)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="881.63" monoisotopic="881.1468"/><formula>C26H42N7O19P3S1</formula><sprotFT><![CDATA[(Bindin...
<oneModRes name="O-(sn-1-glycerophosphoryl)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="154.06" monoisotopic="154.0031"/><formula>C3H7N0O5P1</formula><sprotFT><![CDATA[(Binding site: sn-1-glyce...
<oneModRes name="O-D-glucuronosyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="176.12" monoisotopic="176.0321"/><formula>C6H8N0O6</formula><sprotFT><![CDATA[(Not available|CARBOHYD O-linked (Glc...
<oneModRes name="O-acetyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT></o...
<oneModRes name="O-decanoyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="154.25" monoisotopic="154.1358"/><formula>C10H18N0O1</formula><sprotFT><![CDATA[(Not available|LIPID O-decanoyl serine).*...
<oneModRes name="O-decanoyl-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="154.25" monoisotopic="154.1358"/><formula>C10H18N0O1</formula><sprotFT><![CDATA[(Not available|LIPID O-decanoyl threon...
<oneModRes name="O-glycosyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="203.19 +" monoisotopic="203.0793 +"/><formula>C8H13N1O5+</formula><sprotFT><![CDATA[(Binding site: carbohydrate (Ser) (co...
<oneModRes name="O-glycosyl-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="203.19 +" monoisotopic="203.0793 +"/><formula>C8H13N1O5+</formula><sprotFT><![CDATA[(Binding site: carbohydrate (Thr) ...
<oneModRes name="O-octanoyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="126.20" monoisotopic="126.1045"/><formula>C8H14N0O1</formula><sprotFT><![CDATA[(Binding site: octanoate (Ser) (covalent)|...
<oneModRes name="O-octanoyl-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="126.20" monoisotopic="126.1045"/><formula>C8H14N0O1</formula><sprotFT><![CDATA[(Not available|LIPID O-octanoyl threoni...
<oneModRes name="O-palmitoyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="238.41" monoisotopic="238.2297"/><formula>C16H30N0O1</formula><sprotFT><![CDATA[(Binding site: fatty acid (Ser) (covalen...
<oneModRes name="O-palmitoyl-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="238.41" monoisotopic="238.2297"/><formula>C16H30N0O1</formula><sprotFT><![CDATA[(Binding site: fatty acid (Thr) (cova...
<oneModRes name="O-phospho-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotFT><![CDATA[(Active site: Ser (phosphoserine intermediat...
<oneModRes name="O-phospho-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotFT><![CDATA[(Binding site: phosphate (Thr) (covalent)...
<oneModRes name="O-sulfo-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="80.06" monoisotopic="79.9568"/><formula>C0H0N0O3S1</formula><sprotFT><![CDATA[(Not available|MOD_RES Sulfoserine).*]]></spro...
<oneModRes name="O-sulfo-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="80.06" monoisotopic="79.9568"/><formula>C0H0N0O3S1</formula><sprotFT><![CDATA[(Not available|MOD_RES Sulfothreonine).*]]>...
<oneModRes name="O3-(riboflavin phosphoryl)-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="438.33" monoisotopic="438.0940"/><formula>C17H19N4O8P1</formula><sprotFT><![CDATA[(Not available|MOD_RES ...
<oneModRes name="O3-(riboflavin phosphoryl)-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="438.33" monoisotopic="438.0940"/><formula>C17H19N4O8P1</formula><sprotFT><![CDATA[(Not available|MOD_R...
<oneModRes name="O3-phosphopantetheine-L-serine" type="aaModif"><description>Crystal structure of butyryl-ACP I62M mutant.</description><site><residue>S</residue></site><delta average="340.33" monoisotopic="340.0858"/><formula>C11H21N2O6P1S1</formula...
<oneModRes name="O4-glycosyl-L-hydroxyproline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="148.11 +" monoisotopic="148.0372 +"/><formula>C5H8N0O5+</formula><sprotFT><![CDATA[(Not available|CARBOHYD O-lin...
<oneModRes name="O4p-(8alpha-FAD)-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="783.53" monoisotopic="783.1414"/><formula>C27H31N9O15P2</formula><sprotFT><![CDATA[(Not available|MOD_RES O-8alph...
<oneModRes name="O4p-(phospho-3p-DNA)-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="79.98 +" monoisotopic="79.9663 +"/><formula>C0H1N0O3P1+</formula><sprotFT><![CDATA[(Active site: Tyr (covalen...
<oneModRes name="O4p-(phospho-5p-DNA)-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="79.98 +" monoisotopic="79.9663 +"/><formula>C0H1N0O3P1+</formula><sprotFT><![CDATA[(Binding site: phosphoryl-...
<oneModRes name="O4p-(phospho-5p-RNA)-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="79.98 +" monoisotopic="79.9663 +"/><formula>C0H1N0O3P1+</formula><sprotFT><![CDATA[(Binding site: phosphoryl-...
<oneModRes name="O4p-(phospho-5p-adenosine)-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="329.21" monoisotopic="329.0525"/><formula>C10H12N5O6P1</formula><sprotFT><![CDATA[(Binding site: AMP (T...
<oneModRes name="O4p-(phospho-5p-uridine)-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="306.17" monoisotopic="306.0253"/><formula>C9H11N2O8P1</formula><sprotFT><![CDATA[(Binding site: UMP (Tyr)...
<oneModRes name="O4p-glycosyl-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="162.14 +" monoisotopic="162.0528 +"/><formula>C6H10N0O5+</formula><sprotFT><![CDATA[(Binding site: carbohydrate (Tyr)...
<oneModRes name="O4p-phospho-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotFT><![CDATA[(Binding site: phosphate (Tyr) (covalent...
<oneModRes name="O4p-sulfo-L-tyrosine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="80.06" monoisotopic="79.9568"/><formula>C0H0N0O3S1</formula><sprotFT><![CDATA[(Binding site: sulfate (Tyr) (covalent)|MO...
<oneModRes name="O5-glucosylgalactosyl-L-hydroxylysine" type="aaModif"><description></description><site><residue>K</residue></site><delta average="340.28" monoisotopic="340.1005"/><formula>C12H20N0O11</formula><sprotFT><![CDATA[(Binding site: carbohy...
<oneModRes name="S-(2-aminovinyl)-3-methyl-D-cysteine" type="aaModif"><description></description><siteRegexp>C.*?T</siteRegexp><delta average="-64.04" monoisotopic="-64.0160"/><formula>C-1H-4N0O-3S0</formula><sprotFT><![CDATA[(Cross-link: (2S,3S,5Z)-...
<oneModRes name="S-(2-aminovinyl)-D-cysteine" type="aaModif"><description></description><siteRegexp>C.*?S</siteRegexp><delta average="-64.04" monoisotopic="-64.0160"/><formula>C-1H-4N0O-3S0</formula><sprotFT><![CDATA[(Cross-link: (S,Z)-S-(2-aminoviny...
<oneModRes name="S-(4a-FMN)-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="456.34" monoisotopic="456.1046"/><formula>C17H21N4O9P1S0</formula><sprotFT><![CDATA[(Not available|MOD_RES S-4a-FMN cys...
<oneModRes name="S-(6-FMN)-L-cysteine" type="aaModif"><description>Correlation of X-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase.</description><site><residue>C</residue></site><delta average="454.33" monoisotopic=...
<oneModRes name="S-(8alpha-FAD)-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="783.53" monoisotopic="783.1414"/><formula>C27H31N9O15P2S0</formula><sprotFT><![CDATA[(Modified site: S-(8alpha-FAD)...
<oneModRes name="S-(ADP-ribosyl)-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="541.30" monoisotopic="541.0610"/><formula>C15H21N5O13P2S0</formula><sprotFT><![CDATA[(Modified site: ADP-ribosylcy...
<oneModRes name="S-(L-isoglutamyl)-L-cysteine" type="aaModif"><description></description><siteRegexp>C.*?Q</siteRegexp><delta average="-17.03" monoisotopic="-17.0265"/><formula>C0H-3N-1O0S0</formula><sprotFT><![CDATA[(Cross-link: thiolester (Cys-Gln)...
<oneModRes name="S-12-hydroxyfarnesyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="220.35" monoisotopic="220.1827"/><formula>C15H24N0O1S0</formula><sprotFT><![CDATA[(Binding site: farnesyl (Cy...
<oneModRes name="S-4-hydroxycinnamyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="146.14" monoisotopic="146.0368"/><formula>C9H6N0O2S0</formula><sprotFT><![CDATA[(Binding site: 4-hydroxycinnam...
<oneModRes name="S-[5p-(L-tryptoph-6p-yl)-L-tyrosin-3p-yl]-L-methionin-S-ium" type="aaModif"><description></description><siteRegexp>M.*?W.*?Y</siteRegexp><delta average="-3.02" monoisotopic="-3.0235"/><formula>C0H-3N0O0S0</formula><sprotFT><![CDATA[(...
<oneModRes name="S-acetyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="42.04" monoisotopic="42.0106"/><formula>C2H2N0O1S0</formula><sprotFT><![CDATA[(Active site: Cys (S-acetylcysteine interme...
<oneModRes name="S-amidino-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="42.04" monoisotopic="42.0218"/><formula>C1H2N2O0S0</formula><sprotFT><![CDATA[(Not available|ACT_SITE Amidino-cysteine i...
<oneModRes name="S-carbamoyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="43.02" monoisotopic="43.0058"/><formula>C1H1N1O1S0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></spro...
<oneModRes name="S-cyano-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="25.01" monoisotopic="24.9952"/><formula>C1H-1N1O0S0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></sprotFT...
<oneModRes name="S-diacylglycerol-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="576.94" monoisotopic="576.5117"/><formula>C37H68N0O4S0</formula><sprotFT><![CDATA[(Binding site: sn-2,3-diacylgly...
<oneModRes name="S-diphytanylglycerol diether-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="635.14" monoisotopic="634.6628"/><formula>C43H86N0O2S0</formula><sprotFT><![CDATA[(Binding site: sn-2...
<oneModRes name="S-farnesyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="204.35" monoisotopic="204.1878"/><formula>C15H24N0O0S0</formula><sprotFT><![CDATA[(Binding site: farnesyl (Cys) (covale...
<oneModRes name="S-geranylgeranyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="272.47" monoisotopic="272.2504"/><formula>C20H32N0O0S0</formula><sprotFT><![CDATA[(Binding site: geranyl-geranyl ...
<oneModRes name="S-glycosyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="162.14 +" monoisotopic="162.0528 +"/><formula>C6H10N0O5S0+</formula><sprotFT><![CDATA[(Binding site: carbohydrate (Cys)...
<oneModRes name="S-glycyl-L-cysteine" type="aaModif"><description></description><siteRegexp>C.*?G</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: thiolester carboxyl end (Gly)...
<oneModRes name="S-methyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0S0</formula><sprotFT><![CDATA[(Binding site: methyl (Cys) (covalent)|Acti...
<oneModRes name="S-myristoyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="210.36" monoisotopic="210.1984"/><formula>C14H26N0O1S0</formula><sprotFT><![CDATA[(Not available|Not available).*]]></...
<oneModRes name="S-nitrosyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="29.00" monoisotopic="28.9902"/><formula>C0H-1N1O1S0</formula><sprotFT><![CDATA[(Binding site: nitrosonium (Cys) (covale...
<oneModRes name="S-palmitoleyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="236.39" monoisotopic="236.2140"/><formula>C16H28N0O1S0</formula><sprotFT><![CDATA[(Not available|Not available).*]]>...
<oneModRes name="S-palmitoyl-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="238.41" monoisotopic="238.2297"/><formula>C16H30N0O1S0</formula><sprotFT><![CDATA[(Binding site: palmitate (Cys) (cova...
<oneModRes name="S-phospho-L-cysteine" type="aaModif"><description>Crystal structure of human protein tyrosine phosphatase 1B.</description><site><residue>C</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1S0</formula...
<oneModRes name="S-phycobiliviolin-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="586.68" monoisotopic="586.2791"/><formula>C33H38N4O6S0</formula><sprotFT><![CDATA[(Binding site: phycobiliviolin...
<oneModRes name="S-phycocyanobilin-L-cysteine" type="aaModif"><description>Structure of phycocyanin from Cyanidium caldarium at 1.65A resolution.</description><site><residue>C</residue></site><delta average="586.68" monoisotopic="586.2791"/><formula>...
<oneModRes name="S-phycoerythrobilin-L-cysteine" type="aaModif"><description>Crystal structure of R-phycoerythrin from Polysiphonia at 2.8 A resolution.</description><site><residue>C</residue></site><delta average="588.70" monoisotopic="588.2947"/><f...
<oneModRes name="S-phytochromobilin-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="584.66" monoisotopic="584.2634"/><formula>C33H36N4O6S0</formula><sprotFT><![CDATA[(Binding site: phytochromobil...
<oneModRes name="S-selenyl-L-cysteine" type="aaModif"><description>Carbon monoxide dehydrogenase from Hydrogenophaga pseudoflava.</description><site><residue>C</residue></site><delta average="78.96" monoisotopic="79.9165"/><formula>C0H0N0O0S0Se1</for...
<oneModRes name="S-sulfo-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="80.06" monoisotopic="79.9568"/><formula>C0H0N0O3S1</formula><sprotFT><![CDATA[(Active site: Cys (sulfocysteine intermediat...
<oneModRes name="alpha-1-microglobulin-Ig alpha complex chromophore" type="aaModif"><description></description><siteRegexp>C.*?C</siteRegexp><delta average="-2.02 +" monoisotopic="-2.0156 +"/><formula>C0H-2N0O0S0+</formula><sprotFT><![CDATA[(Cross-li...
<oneModRes name="bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide" type="aaModif"><description>Architecture of the photosynthetic oxygen evolving center.</description><siteRegexp>D.*?D.*?E.*?E.*?E.*?H</siteRegexp><delta a...
<oneModRes name="bis-L-cysteinyl L-N3p-histidino L-serinyl tetrairon tetrasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?H.*?S</siteRegexp><delta average="347.60" monoisotopic="347.5967"/><formula>C0Fe4H-4N0O0S4</formula><spro...
<oneModRes name="bis-L-cysteinyl bis-L-histidino diiron disulfide" type="aaModif"><description>Structure of a water soluble fragment of the Rieske iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1-complex.</description><siteRegexp>...
<oneModRes name="chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-1.01 +" monoisotopic="-1.0078 +"/><formula>C0H-1N0O0+</formu...
<oneModRes name="cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester" type="aaModif"><description></description><site><residue>D</residue></site><delta average="294.39" monoisotopic="294.1831"/><formula>C17H26N0O4</formula><sprotFT><![C...
<oneModRes name="dehydroalanine" type="aaModif"><description></description><site><residue>Y</residue></site><delta average="-94.11" monoisotopic="-94.0419"/><formula>C-6H-6N0O-1</formula><sprotFT><![CDATA[(Modified site: dehydroalanine (Ser)|Modified...
<oneModRes name="dermatan 4-sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-1.01 +" monoisotopic="-1.0078 +"/><formula>C0H-1N0O0+</formul...
<oneModRes name="dihydroxyheme-L-aspartate ester-L-glutamate ester" type="aaModif"><description></description><siteRegexp>D.*?E</siteRegexp><delta average="612.46" monoisotopic="612.1460"/><formula>C34Fe1H28N4O4</formula><sprotFT><![CDATA[(Binding si...
<oneModRes name="dihydroxyheme-L-aspartate ester-L-glutamate ester-L-methionine sulfonium" type="aaModif"><description>X-ray crystal structure of canine myeloperoxidase at 3 A resolution.</description><siteRegexp>D.*?E.*?M</siteRegexp><delta average=...
<oneModRes name="dipyrrolylmethanemethyl-L-cysteine" type="aaModif"><description>Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.</description><site><residue>C</residue></site><delta avera...
<oneModRes name="glycine" type="aaModif"><description></description><site><residue>G</residue></site><delta average="0.98" monoisotopic="0.9840"/><formula>C0H-1N-1O1</formula><sprotFT><![CDATA[(Active site: Gly (stable glycyl radical)|MOD_RES Glycine...
<oneModRes name="glycine amide" type="aaModif"><description></description><site><residue>G</residue></site><delta average="-0.98" monoisotopic="-0.9840"/><formula>C0H1N1O-1</formula><sprotFT><![CDATA[(Modified site: amidated carboxyl end (Gly)|Modifi...
<oneModRes name="glycine cholesterol ester" type="aaModif"><description></description><site><residue>G</residue></site><delta average="368.64" monoisotopic="368.3443"/><formula>C27H44N0O0</formula><sprotFT><![CDATA[(Not available|LIPID Cholesterol gl...
<oneModRes name="glycine oxazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>G.*?S</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1</formula><sprotFT><![CDATA[(Cross-link: oxazole (Gly-Ser)|CR...
<oneModRes name="glycine thiazolecarboxylic acid" type="aaModif"><description></description><siteRegexp>C.*?G</siteRegexp><delta average="-20.03" monoisotopic="-20.0262"/><formula>C0H-4N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: thiazole (Gly-Cys...
<oneModRes name="heme P460-bis-L-cysteine-L-lysine" type="aaModif"><description></description><siteRegexp>C.*?C.*?K</siteRegexp><delta average="614.47" monoisotopic="614.1616"/><formula>C34Fe1H30N4O4S0</formula><sprotFT><![CDATA[(Binding site: heme P...
<oneModRes name="heme P460-bis-L-cysteine-L-tyrosine" type="aaModif"><description>X-Ray structure of hydroxylamine oxidoreductase.</description><siteRegexp>C.*?C.*?Y</siteRegexp><delta average="614.47" monoisotopic="614.1616"/><formula>C34Fe1H30N4O4S...
<oneModRes name="heme-L-cysteine" type="aaModif"><description></description><site><residue>C</residue></site><delta average="616.49" monoisotopic="616.1773"/><formula>C34Fe1H32N4O4S0</formula><sprotFT><![CDATA[(Binding site: heme (Cys) (covalent)|BIN...
<oneModRes name="heme-bis-L-cysteine" type="aaModif"><description></description><siteRegexp>C.*?C</siteRegexp><delta average="616.49" monoisotopic="616.1773"/><formula>C34Fe1H32N4O4S0</formula><sprotFT><![CDATA[(Binding site: heme (Cys) (covalent)|BI...
<oneModRes name="heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-1.01 +" monoisotopic="-1.0078 +"/><formula>C0H-1N0O0+</formula><...
<oneModRes name="heptakis-L-histidino tetracopper mu4-sulfide hydroxide" type="aaModif"><description>Crystal structure of nitrous oxide reductase from Pseudomonas nautica, at 2.4A resolution.</description><siteRegexp>H.*?H.*?H.*?H.*?H.*?H.*?H</siteRe...
<oneModRes name="hexakis-L-cysteinyl L-serinyl octairon heptasulfide" type="aaModif"><description>Nitrogenase MoFe protein from Azotobacter vinelandii.</description><siteRegexp>C.*?C.*?C.*?C.*?C.*?C.*?S</siteRegexp><delta average="663.14" monoisotopi...
<oneModRes name="hexakis-L-cysteinyl hexairon hexasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C.*?C.*?C</siteRegexp><delta average="521.41" monoisotopic="521.3951"/><formula>C0Fe6H-6N0O0S6</formula><sprotFT><![CDATA[(No...
<oneModRes name="hexakis-L-cysteinyl triiron trisulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C.*?C.*?C</siteRegexp><delta average="257.68" monoisotopic="257.6741"/><formula>C0Fe3H-6N0O0S3</formula><sprotFT><![CDATA[(Not ...
<oneModRes name="hydroxyheme-L-glutamate ester" type="aaModif"><description></description><site><residue>E</residue></site><delta average="614.47" monoisotopic="614.1616"/><formula>C34Fe1H30N4O4</formula><sprotFT><![CDATA[(Not available|BINDING Heme ...
<oneModRes name="keratan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-threonine" type="aaModif"><description></description><site><residue>T</residue></site><delta average="-1.01 +" monoisotopic="-1.0078 +"/><formula>C0H-1N0O0+</formul...
<oneModRes name="lactic acid" type="aaModif"><description></description><site><residue>S</residue></site><delta average="-15.01" monoisotopic="-15.0109"/><formula>C0H-1N-1O0</formula><sprotFT><![CDATA[(Modified site: lactic acid (Ser) (in mature form...
<oneModRes name="meso-lanthionine" type="aaModif"><description></description><siteRegexp>C.*?S</siteRegexp><delta average="-18.02" monoisotopic="-18.0106"/><formula>C0H-2N0O-1S0</formula><sprotFT><![CDATA[(Cross-link: sn-(2S,6R)-lanthionine (Ser-Cys)...
<oneModRes name="omega-N,omega-N-dimethyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="28.05" monoisotopic="28.0313"/><formula>C2H4N0O0</formula><sprotFT><![CDATA[(Modified site: omega-N,omega...
<oneModRes name="omega-N,omega-Np-dimethyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="28.05" monoisotopic="28.0313"/><formula>C2H4N0O0</formula><sprotFT><![CDATA[(Modified site: omega-N,omeg...
<oneModRes name="omega-N-(ADP-ribosyl)-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="541.30" monoisotopic="541.0610"/><formula>C15H21N5O13P2</formula><sprotFT><![CDATA[(Modified site: ADP-ribos...
<oneModRes name="omega-N-glycosyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="162.14" monoisotopic="162.0528"/><formula>C6H10N0O5</formula><sprotFT><![CDATA[(Not available|CARBOHYD N-linked (...
<oneModRes name="omega-N-methyl-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="14.03" monoisotopic="14.0157"/><formula>C1H2N0O0</formula><sprotFT><![CDATA[(Modified site: omega-N-methylarginine ...
<oneModRes name="omega-N-phospho-L-arginine" type="aaModif"><description></description><site><residue>R</residue></site><delta average="79.98" monoisotopic="79.9663"/><formula>C0H1N0O3P1</formula><sprotFT><![CDATA[(Binding site: phosphate (Arg) (cova...
<oneModRes name="pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfide" type="aaModif"><description>Crystal structure of a Ni-containing carbon monoxide dehydrogenase from Carboxydothermus hydrogenoformans.</description><siteRegexp>C.*?C.*?C...
<oneModRes name="phycoerythrobilin-bis-L-cysteine" type="aaModif"><description></description><siteRegexp>C.*?C</siteRegexp><delta average="586.68" monoisotopic="586.2791"/><formula>C33H38N4O6S0</formula><sprotFT><![CDATA[(Binding site: phycoerythrobi...
<oneModRes name="phycourobilin-bis-L-cysteine" type="aaModif"><description>Crystal structure of R-phycoerythrin from Polysiphonia at 2.8 A resolution.</description><siteRegexp>C.*?C</siteRegexp><delta average="586.68" monoisotopic="586.2791"/><formul...
<oneModRes name="pyrroloquinoline quinone" type="aaModif"><description></description><siteRegexp>E.*?Y</siteRegexp><delta average="37.92" monoisotopic="37.9065"/><formula>C0H-10N0O3</formula><sprotFT><![CDATA[(Cross-link: pyrroloquinoline quinone (Gl...
<oneModRes name="pyruvic acid" type="aaModif"><description>Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.</description><site><residue>S</residue></site><delta average="-17.03" monoisotopic="-17.0265"/><for...
<oneModRes name="tetrakis-L-cysteinyl diiron disulfide" type="aaModif"><description>2Fe-2S Ferredoxin from Haloarcula marismortui.</description><siteRegexp>C.*?C.*?C.*?C</siteRegexp><delta average="171.79" monoisotopic="171.7827"/><formula>C0Fe2H-4N0...
<oneModRes name="tetrakis-L-cysteinyl iron" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C</siteRegexp><delta average="51.81" monoisotopic="51.9036"/><formula>C0Fe1H-4N0O0S0</formula><sprotFT><![CDATA[(Binding site: iron (Cys)|ME...
<oneModRes name="tetrakis-L-cysteinyl tetrairon tetrasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C</siteRegexp><delta average="347.60" monoisotopic="347.5967"/><formula>C0Fe4H-4N0O0S4</formula><sprotFT><![CDATA[(Binding...
<oneModRes name="tetrakis-L-cysteinyl triiron tetrasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C</siteRegexp><delta average="291.76" monoisotopic="291.6618"/><formula>C0Fe3H-4N0O0S4</formula><sprotFT><![CDATA[(Not avail...
<oneModRes name="trans-2,3-cis-3,4-dihydroxy-L-proline" type="aaModif"><description></description><site><residue>P</residue></site><delta average="32.00" monoisotopic="31.9898"/><formula>C0H0N0O2</formula><sprotFT><![CDATA[(Modified site: trans-2,3-c...
<oneModRes name="tris-L-cysteinyl L-N1p-histidino tetrairon tetrasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?H</siteRegexp><delta average="347.60" monoisotopic="347.5967"/><formula>C0Fe4H-4N0O0S4</formula><sprotFT><![CD...
<oneModRes name="tris-L-cysteinyl L-N3p-histidino tetrairon tetrasulfide" type="aaModif"><description>Crystal structure of the oxidized form of Ni-Fe hydrogenase.</description><siteRegexp>C.*?C.*?C.*?H</siteRegexp><delta average="347.60" monoisotopic...
<oneModRes name="tris-L-cysteinyl L-arginyl diiron disulfide" type="aaModif"><description>The crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.</description><siteRegexp>C.*?C.*?C.*?R</siteRegexp><delta average="1...
<oneModRes name="tris-L-cysteinyl L-aspartato diiron disulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?D</siteRegexp><delta average="171.79" monoisotopic="171.7827"/><formula>C0Fe2H-4N0O0S2</formula><sprotFT><![CDATA[(Not a...
<oneModRes name="tris-L-cysteinyl L-aspartato tetrairon tetrasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?D</siteRegexp><delta average="347.60" monoisotopic="347.5967"/><formula>C0Fe4H-4N0O0S4</formula><sprotFT><![CDATA[...
<oneModRes name="tris-L-cysteinyl L-cysteine persulfido L-glutamato L-histidino L-serinyl nickel triiron disulfide trioxide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C.*?E.*?H.*?S</siteRegexp><delta average="363.36" monoisoto...
<oneModRes name="tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino nickel triiron disulfide trioxide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C.*?E.*?E.*?H</siteRegexp><delta average="363.36" monoisotopic="3...
<oneModRes name="tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino tetrairon disulfide trioxide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?C.*?E.*?E.*?H</siteRegexp><delta average="360.51" monoisotopic="360.58...
<oneModRes name="tris-L-cysteinyl L-serinyl tetrairon tetrasulfide" type="aaModif"><description></description><siteRegexp>C.*?C.*?C.*?S</siteRegexp><delta average="347.60" monoisotopic="347.5967"/><formula>C0Fe4H-4N0O0S4</formula><sprotFT><![CDATA[(B...
<oneModRes name="tris-L-cysteinyl S-adenosylmethion-N,O-diyl tetrairon tetrasulfide" type="aaModif"><description>The crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.</description><siteRegexp>C.*?C.*?C</siteRegex...
<oneModRes name="tris-L-cysteinyl triiron tetrasulfide" type="aaModif"><description>The NMR solution structure of the 3Fe ferredoxin II from Desulfovibrio gigas, 15 structures.</description><siteRegexp>C.*?C.*?C</siteRegexp><delta average="292.77" mo...
  </modRes>
</inSilicoDefinitions>

lib/InSilicoSpectro/config/insilicodef.xml view on Meta::CPAN

    <oneElement symbol="H+" name="Hydrogen ion" atomicNumber="1">
      <mass monoisotopic="1.00728" average="1.00739"/>
      <isotopes>
        <oneIsotope plus="0" mass="1.00728" abundance="100.00"/>
      </isotopes>
    </oneElement>
  </elements>

  <molecules>
    <oneMolecule symbol="H2O" name="Water">
      <formula>H2O1</formula>
      <mass monoisotopic="18.01056" average="18.01524"/>
    </oneMolecule>
    <oneMolecule symbol="NH3" name="Amine">
      <formula>N1H3</formula>
      <mass monoisotopic="17.03712" average="17.03052"/>
    </oneMolecule>
  </molecules>

  <codons>
    <oneCodon name="Adenine" code1="A"/>
    <oneCodon name="Cytosine" code1="C"/>
    <oneCodon name="Guanine" code1="G"/>
    <oneCodon name="Uracil" code1="U"/>
  </codons>

  <aminoAcids>
    <oneAminoAcid name="Alanine" code3="Ala" code1="A">
      <formula>C3H5ON</formula>
      <mRNACodons>
        <oneMRNACodon>GCA</oneMRNACodon> 
        <oneMRNACodon>GCC</oneMRNACodon> 
        <oneMRNACodon>GCG</oneMRNACodon> 
        <oneMRNACodon>GCU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="71.03711" average="71.0788"/>
      <PK internal="0.0" nterm="7.59" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Arginine" code3="Arg" code1="R">
      <formula>C6H12ON4</formula>
      <mRNACodons>
        <oneMRNACodon>AGA</oneMRNACodon> 
        <oneMRNACodon>AGG</oneMRNACodon> 
        <oneMRNACodon>CGA</oneMRNACodon> 
        <oneMRNACodon>CGC</oneMRNACodon> 
        <oneMRNACodon>CGG</oneMRNACodon> 
        <oneMRNACodon>CGU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="156.10111" average="156.1875"/>
      <PK internal="12.0" nterm="7.50" cterm="3.55" sgnres="+1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Asparagine" code3="Asn" code1="N">
      <formula>C4H6O2N2</formula>
      <mRNACodons>
        <oneMRNACodon>AAC</oneMRNACodon> 
        <oneMRNACodon>AAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="114.04293" average="114.1038"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Aspartic_acid" code3="Asp" code1="D">
      <formula>C4H5O3N</formula>
      <mRNACodons>
        <oneMRNACodon>GAC</oneMRNACodon> 
        <oneMRNACodon>GAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="115.02694" average="115.0886"/>
      <PK internal="4.05" nterm="7.50" cterm="4.55" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Cysteine" code3="Cys" code1="C">
      <formula>C3H5ONS</formula>
      <mRNACodons>
        <oneMRNACodon>UGC</oneMRNACodon> 
        <oneMRNACodon>UGU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="103.00919" average="103.1388"/>
      <PK internal="9.0" nterm="7.50" cterm="3.55" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Glutamic_acid" code3="Glu" code1="E">
      <formula>C5H7O3N</formula>
      <mRNACodons>
        <oneMRNACodon>GAA</oneMRNACodon> 
        <oneMRNACodon>GAG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="129.04259" average="129.1155"/>
      <PK internal="4.45" nterm="7.70" cterm="4.75" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Glutamine" code3="Gln" code1="Q">
      <formula>C5H8O2N2</formula>
      <mRNACodons>
        <oneMRNACodon>CAA</oneMRNACodon> 
        <oneMRNACodon>CAG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="128.05858" average="128.1307"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Glycine" code3="Gly" code1="G">
      <formula>C2H3ON</formula>
      <mRNACodons>
        <oneMRNACodon>GGA</oneMRNACodon> 
        <oneMRNACodon>GGC</oneMRNACodon> 
        <oneMRNACodon>GGG</oneMRNACodon> 
        <oneMRNACodon>GGU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="57.02146" average="57.0519"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Histidine" code3="His" code1="H">
      <formula>C6H7ON3</formula>
      <mRNACodons>
        <oneMRNACodon>CAC</oneMRNACodon> 
        <oneMRNACodon>CAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="137.05891" average="137.1411"/>
      <PK internal="5.98" nterm="7.50" cterm="3.55" sgnres="+1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Isoleucine" code3="Ile" code1="I">
      <formula>C6H11ON</formula>
      <mRNACodons>
        <oneMRNACodon>AUA</oneMRNACodon> 
        <oneMRNACodon>AUC</oneMRNACodon> 
        <oneMRNACodon>AUU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="113.08406" average="113.1594"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Leucine" code3="Leu" code1="L">
      <formula>C6H11ON</formula>
      <mRNACodons>
        <oneMRNACodon>CUA</oneMRNACodon> 
        <oneMRNACodon>CUC</oneMRNACodon> 
        <oneMRNACodon>CUG</oneMRNACodon> 
        <oneMRNACodon>CUU</oneMRNACodon> 
        <oneMRNACodon>UUA</oneMRNACodon> 
        <oneMRNACodon>UUG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="113.08406" average="113.1594"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Lysine" code3="Lys" code1="K">
      <formula>C6H12ON2</formula>
      <mRNACodons>
        <oneMRNACodon>AAA</oneMRNACodon> 
        <oneMRNACodon>AAG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="128.09496" average="128.1741"/>
      <PK internal="10.0" nterm="7.50" cterm="3.55" sgnres="+1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Methionine" code3="Met" code1="M">
      <formula>C5H9ONS</formula>
      <mRNACodons>
        <oneMRNACodon>AUG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="131.04049" average="131.1926"/>
      <PK internal="0.0" nterm="7.00" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Phenylalanine" code3="Phe" code1="F">
      <formula>C9H9ON</formula>
      <mRNACodons>
        <oneMRNACodon>UUC</oneMRNACodon> 
        <oneMRNACodon>UUU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="147.06841" average="147.1766"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Proline" code3="Pro" code1="P">
      <formula>C5H7ON</formula>
      <mRNACodons>
        <oneMRNACodon>CCA</oneMRNACodon> 
        <oneMRNACodon>CCC</oneMRNACodon> 
        <oneMRNACodon>CCG</oneMRNACodon> 
        <oneMRNACodon>CCU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="97.05276" average="97.1167"/>
      <PK internal="0.0" nterm="8.36" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Serine" code3="Ser" code1="S">
      <formula>C3H5O2N</formula>
      <mRNACodons>
        <oneMRNACodon>AGC</oneMRNACodon> 
        <oneMRNACodon>AGU</oneMRNACodon> 
        <oneMRNACodon>UCA</oneMRNACodon> 
        <oneMRNACodon>UCC</oneMRNACodon> 
        <oneMRNACodon>UCG</oneMRNACodon> 
        <oneMRNACodon>UCU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="87.03203" average="87.0782"/>
      <PK internal="0.0" nterm="6.93" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Threonine" code3="Thr" code1="T">
      <formula>C4H7O2N</formula>
      <mRNACodons>
        <oneMRNACodon>ACA</oneMRNACodon> 
        <oneMRNACodon>ACC</oneMRNACodon> 
        <oneMRNACodon>ACG</oneMRNACodon> 
        <oneMRNACodon>ACU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="101.04768" average="101.1051"/>
      <PK internal="0.0" nterm="6.82" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Tryptophan" code3="Trp" code1="W">
      <formula>C11H10ON2</formula>
      <mRNACodons>
        <oneMRNACodon>UGG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="186.07931" average="186.2132"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Tyrosine" code3="Tyr" code1="Y">
      <formula>C9H9O2N</formula>
      <mRNACodons>
        <oneMRNACodon>UAC</oneMRNACodon> 
        <oneMRNACodon>UAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="163.06333" average="163.1760"/>
      <PK internal="10.0" nterm="7.50" cterm="3.55" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Valine" code3="Val" code1="V">
      <formula>C5H9ON</formula>
      <mRNACodons>
        <oneMRNACodon>GUA</oneMRNACodon> 
        <oneMRNACodon>GUC</oneMRNACodon> 
        <oneMRNACodon>GUG</oneMRNACodon> 
        <oneMRNACodon>GUU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="99.06841" average="99.1326"/>
      <PK internal="0.0" nterm="7.44" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
  </aminoAcids>

lib/InSilicoSpectro/config/insilicodef.xml view on Meta::CPAN


<fragTypeDescriptions>
 <fragTypeDefSet readonly="1">

  <series>
    <oneSeries name="a">
      <terminus>N</terminus>
      <deltaMass monoisotopic="-27.99491" average="-28.0104"/>
      <firstFragment>2</firstFragment>
      <lastFragment>2</lastFragment>
      <formula>O-1C-1</formula>
    </oneSeries>
    <oneSeries name="b">
      <terminus>N</terminus>
      <firstFragment>2</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="0" average="0"/>
      <formula></formula>
    </oneSeries>
    <oneSeries name="c">
      <terminus>N</terminus>
      <firstFragment>2</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="17.02656" average="17.03052"/>
      <formula>NH3</formula>
    </oneSeries>
    <oneSeries name="x">
      <terminus>C</terminus>
      <firstFragment>1</firstFragment>
      <lastFragment>2</lastFragment>
      <formula>COH-1</formula>
      <deltaMass monoisotopic="43.98982" average="44.0098"/>
    </oneSeries>
    <oneSeries name="y">
      <terminus>C</terminus>
      <firstFragment>1</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="18.0105746" average="18.01418"/>
      <formula>H</formula>
    </oneSeries>
    <oneSeries name="z">
      <terminus>C</terminus>
      <firstFragment>1</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="1.9912946" average="1.99108"/>
      <formula>N-1H-1</formula>
    </oneSeries>
  </series>

  <losses>
    <oneLoss name="NH3">
      <residues aa="NQR"/>
      <deltaMass monoisotopic="17.03712" average="17.03052"/>
      <formula>N-1H-3</formula>
    </oneLoss>
    <oneLoss name="H2O">
      <residues aa="ST"/>
      <deltaMass monoisotopic="18.01056" average="18.01524"/>
      <formula>H-2O-1</formula>
    </oneLoss>
  </losses>

  <fragTypes>
    <oneFragType name="a" series="a" charge="1"/>
     <oneFragType name="a++" series="a" charge="2"/>
     <oneFragType name="a+++" series="a" charge="3"/>
    <oneFragType name="a-NH3" series="a" charge="1">
      <loss name="NH3" repeat="1"/>
    </oneFragType>

scripts/importResid.pl view on Meta::CPAN

  $parser->parse(\*F);
  close(F);
}

InSilicoSpectro::saveInSilicoDef($dest);

# ------------------------------ XML --------------------------

my ($curChar, $eNum);
my ($id, $myId, $correction, $weightType, $isSpFeature, $name, $alternateName, $description);
my ($formula, $avgDelta, $monoDelta, $seqSpecificity, @feature);

sub Text
{
  $curChar .= $_;

} # Text


sub StartTag
{

scripts/importResid.pl view on Meta::CPAN

  if ($el eq 'Name'){
    $name = $curChar;
  }
  elsif ($el eq 'AlternateName'){
    $alternateName = $curChar;
  }
  elsif ($el eq 'Description'){
    $description = $curChar;
  }
  elsif (($el eq 'Formula') && defined($correction)){
    $formula = $curChar;
    $formula=~s/\s//g;
  }
  elsif (($el eq 'Weight') && defined($correction)){
    if ($weightType eq 'chemical'){
      $avgDelta = $curChar;
    }
    else{
      $monoDelta = $curChar;
    }
  }
  elsif ($el eq 'CorrectionBlock'){

scripts/importResid.pl view on Meta::CPAN

      $mr->{regexpStr}=$seqSpecificity;
    }elsif(length($seqSpecificity)>1){
      my ($aa, $rem)=split //, $seqSpecificity, 2;
      $mr->{regexpStr}="$aa(?=$rem)";
    }else{
      $mr->{site}{residue}=$seqSpecificity;
    }
    $mr->{delta_monoisotopic}=$monoDelta;
    $mr->{delta_average}=$avgDelta;
    $mr->{sprotFT}="(".(join('|', @feature)).").*";
    $mr->{formula}=$formula;
  }

} # EndTag

t/InSilico/insilicodef-test.xml view on Meta::CPAN

    <oneElement symbol="H+" name="Hydrogen ion" atomicNumber="1">
      <mass monoisotopic="1.00728" average="1.00739"/>
      <isotopes>
        <oneIsotope plus="0" mass="1.00728" abundance="100.00"/>
      </isotopes>
    </oneElement>
  </elements>

  <molecules>
    <oneMolecule symbol="H2O" name="Water">
      <formula>H2O1</formula>
      <mass monoisotopic="18.01056" average="18.01524"/>
    </oneMolecule>
    <oneMolecule symbol="NH3" name="Amine">
      <formula>N1H3</formula>
      <mass monoisotopic="17.03712" average="17.03052"/>
    </oneMolecule>
  </molecules>

  <codons>
    <oneCodon name="Adenine" code1="A"/>
    <oneCodon name="Cytosine" code1="C"/>
    <oneCodon name="Guanine" code1="G"/>
    <oneCodon name="Uracil" code1="U"/>
  </codons>

  <aminoAcids>
    <oneAminoAcid name="Alanine" code3="Ala" code1="A">
      <formula>C3H5ON</formula>
      <mRNACodons>
        <oneMRNACodon>GCA</oneMRNACodon> 
        <oneMRNACodon>GCC</oneMRNACodon> 
        <oneMRNACodon>GCG</oneMRNACodon> 
        <oneMRNACodon>GCU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="71.03711" average="71.0788"/>
      <PK internal="0.0" nterm="7.59" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Arginine" code3="Arg" code1="R">
      <formula>C6H12ON4</formula>
      <mRNACodons>
        <oneMRNACodon>AGA</oneMRNACodon> 
        <oneMRNACodon>AGG</oneMRNACodon> 
        <oneMRNACodon>CGA</oneMRNACodon> 
        <oneMRNACodon>CGC</oneMRNACodon> 
        <oneMRNACodon>CGG</oneMRNACodon> 
        <oneMRNACodon>CGU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="156.10111" average="156.1875"/>
      <PK internal="12.0" nterm="7.50" cterm="3.55" sgnres="+1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Asparagine" code3="Asn" code1="N">
      <formula>C4H6O2N2</formula>
      <mRNACodons>
        <oneMRNACodon>AAC</oneMRNACodon> 
        <oneMRNACodon>AAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="114.04293" average="114.1038"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Aspartic_acid" code3="Asp" code1="D">
      <formula>C4H5O3N</formula>
      <mRNACodons>
        <oneMRNACodon>GAC</oneMRNACodon> 
        <oneMRNACodon>GAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="115.02694" average="115.0886"/>
      <PK internal="4.05" nterm="7.50" cterm="4.55" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Cysteine" code3="Cys" code1="C">
      <formula>C3H5ONS</formula>
      <mRNACodons>
        <oneMRNACodon>UGC</oneMRNACodon> 
        <oneMRNACodon>UGU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="103.00919" average="103.1388"/>
      <PK internal="9.0" nterm="7.50" cterm="3.55" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Glutamic_acid" code3="Glu" code1="E">
      <formula>C5H7O3N</formula>
      <mRNACodons>
        <oneMRNACodon>GAA</oneMRNACodon> 
        <oneMRNACodon>GAG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="129.04259" average="129.1155"/>
      <PK internal="4.45" nterm="7.70" cterm="4.75" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Glutamine" code3="Gln" code1="Q">
      <formula>C5H8O2N2</formula>
      <mRNACodons>
        <oneMRNACodon>CAA</oneMRNACodon> 
        <oneMRNACodon>CAG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="128.05858" average="128.1307"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Glycine" code3="Gly" code1="G">
      <formula>C2H3ON</formula>
      <mRNACodons>
        <oneMRNACodon>GGA</oneMRNACodon> 
        <oneMRNACodon>GGC</oneMRNACodon> 
        <oneMRNACodon>GGG</oneMRNACodon> 
        <oneMRNACodon>GGU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="57.02146" average="57.0519"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Histidine" code3="His" code1="H">
      <formula>C6H7ON3</formula>
      <mRNACodons>
        <oneMRNACodon>CAC</oneMRNACodon> 
        <oneMRNACodon>CAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="137.05891" average="137.1411"/>
      <PK internal="5.98" nterm="7.50" cterm="3.55" sgnres="+1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Isoleucine" code3="Ile" code1="I">
      <formula>C6H11ON</formula>
      <mRNACodons>
        <oneMRNACodon>AUA</oneMRNACodon> 
        <oneMRNACodon>AUC</oneMRNACodon> 
        <oneMRNACodon>AUU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="113.08406" average="113.1594"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Leucine" code3="Leu" code1="L">
      <formula>C6H11ON</formula>
      <mRNACodons>
        <oneMRNACodon>CUA</oneMRNACodon> 
        <oneMRNACodon>CUC</oneMRNACodon> 
        <oneMRNACodon>CUG</oneMRNACodon> 
        <oneMRNACodon>CUU</oneMRNACodon> 
        <oneMRNACodon>UUA</oneMRNACodon> 
        <oneMRNACodon>UUG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="113.08406" average="113.1594"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Lysine" code3="Lys" code1="K">
      <formula>C6H12ON2</formula>
      <mRNACodons>
        <oneMRNACodon>AAA</oneMRNACodon> 
        <oneMRNACodon>AAG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="128.09496" average="128.1741"/>
      <PK internal="10.0" nterm="7.50" cterm="3.55" sgnres="+1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Methionine" code3="Met" code1="M">
      <formula>C5H9ONS</formula>
      <mRNACodons>
        <oneMRNACodon>AUG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="131.04049" average="131.1926"/>
      <PK internal="0.0" nterm="7.00" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Phenylalanine" code3="Phe" code1="F">
      <formula>C9H9ON</formula>
      <mRNACodons>
        <oneMRNACodon>UUC</oneMRNACodon> 
        <oneMRNACodon>UUU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="147.06841" average="147.1766"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Proline" code3="Pro" code1="P">
      <formula>C5H7ON</formula>
      <mRNACodons>
        <oneMRNACodon>CCA</oneMRNACodon> 
        <oneMRNACodon>CCC</oneMRNACodon> 
        <oneMRNACodon>CCG</oneMRNACodon> 
        <oneMRNACodon>CCU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="97.05276" average="97.1167"/>
      <PK internal="0.0" nterm="8.36" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Serine" code3="Ser" code1="S">
      <formula>C3H5O2N</formula>
      <mRNACodons>
        <oneMRNACodon>AGC</oneMRNACodon> 
        <oneMRNACodon>AGU</oneMRNACodon> 
        <oneMRNACodon>UCA</oneMRNACodon> 
        <oneMRNACodon>UCC</oneMRNACodon> 
        <oneMRNACodon>UCG</oneMRNACodon> 
        <oneMRNACodon>UCU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="87.03203" average="87.0782"/>
      <PK internal="0.0" nterm="6.93" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Threonine" code3="Thr" code1="T">
      <formula>C4H7O2N</formula>
      <mRNACodons>
        <oneMRNACodon>ACA</oneMRNACodon> 
        <oneMRNACodon>ACC</oneMRNACodon> 
        <oneMRNACodon>ACG</oneMRNACodon> 
        <oneMRNACodon>ACU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="101.04768" average="101.1051"/>
      <PK internal="0.0" nterm="6.82" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Tryptophan" code3="Trp" code1="W">
      <formula>C11H10ON2</formula>
      <mRNACodons>
        <oneMRNACodon>UGG</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="186.07931" average="186.2132"/>
      <PK internal="0.0" nterm="7.50" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Tyrosine" code3="Tyr" code1="Y">
      <formula>C9H9O2N</formula>
      <mRNACodons>
        <oneMRNACodon>UAC</oneMRNACodon> 
        <oneMRNACodon>UAU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="163.06333" average="163.1760"/>
      <PK internal="10.0" nterm="7.50" cterm="3.55" sgnres="-1.0"/>
    </oneAminoAcid>
    <oneAminoAcid name="Valine" code3="Val" code1="V">
      <formula>C5H9ON</formula>
      <mRNACodons>
        <oneMRNACodon>GUA</oneMRNACodon> 
        <oneMRNACodon>GUC</oneMRNACodon> 
        <oneMRNACodon>GUG</oneMRNACodon> 
        <oneMRNACodon>GUU</oneMRNACodon>
      </mRNACodons>
      <mass monoisotopic="99.06841" average="99.1326"/>
      <PK internal="0.0" nterm="7.44" cterm="3.55" sgnres="0.0"/>
    </oneAminoAcid>
  </aminoAcids>

t/InSilico/insilicodef-test.xml view on Meta::CPAN


<fragTypeDescriptions>
 <fragTypeDefSet readonly="1">

  <series>
    <oneSeries name="a">
      <terminus>N</terminus>
      <deltaMass monoisotopic="-27.99491" average="-28.0104"/>
      <firstFragment>2</firstFragment>
      <lastFragment>2</lastFragment>
      <formula>O-1C-1</formula>
    </oneSeries>
    <oneSeries name="b">
      <terminus>N</terminus>
      <firstFragment>2</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="0" average="0"/>
      <formula></formula>
    </oneSeries>
    <oneSeries name="c">
      <terminus>N</terminus>
      <firstFragment>2</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="17.02656" average="17.03052"/>
      <formula>NH3</formula>
    </oneSeries>
    <oneSeries name="x">
      <terminus>C</terminus>
      <firstFragment>1</firstFragment>
      <lastFragment>2</lastFragment>
      <formula>COH-1</formula>
      <deltaMass monoisotopic="43.98982" average="44.0098"/>
    </oneSeries>
    <oneSeries name="y">
      <terminus>C</terminus>
      <firstFragment>1</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="18.0105746" average="18.01418"/>
      <formula>H</formula>
    </oneSeries>
    <oneSeries name="z">
      <terminus>C</terminus>
      <firstFragment>1</firstFragment>
      <lastFragment>2</lastFragment>
      <deltaMass monoisotopic="1.9912946" average="1.99108"/>
      <formula>N-1H-1</formula>
    </oneSeries>
  </series>

  <losses>
    <oneLoss name="NH3">
      <residues aa="NQR"/>
      <deltaMass monoisotopic="17.03712" average="17.03052"/>
      <formula>N-1H-3</formula>
    </oneLoss>
    <oneLoss name="H2O">
      <residues aa="ST"/>
      <deltaMass monoisotopic="18.01056" average="18.01524"/>
      <formula>H-2O-1</formula>
    </oneLoss>
  </losses>

  <fragTypes>
    <oneFragType name="a" series="a" charge="1"/>
     <oneFragType name="a++" series="a" charge="2"/>
     <oneFragType name="a+++" series="a" charge="3"/>
    <oneFragType name="a-NH3" series="a" charge="1">
      <loss name="NH3" repeat="1"/>
    </oneFragType>

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