"Meh, David" wrote:
>> I'm trying to model a peptide which contains sulfated tyrosine residues to a
> known crystal structure from the PDB using Swiss PDB Viewer. I can get an
> okay fit, but my sequence remains unsulfated in the model and I'm sure the
> fit would be better if it were sulfated. The peptide sequence is imported as
> a FASTA code with only single letter abbreviation. Is there a single letter
> code for Y-SO3, or can I edit the Swiss PDB viewer to incorporate the
> sulfation?
> Thanks for your help,
> Dave
If there is a structure in the PDB database which incorporates a
sulphated tyrosine then you could look in the PDB text file and see how
that annotates the sulphation. I suspect that the extra atoms will
probably be added to the tyrosine using the HETATOM tag and specifying
the correct connect information. What you could try is saving the extra
groups from the tyrosine to a seperate file, superimposing this onto the
tyrosine in the model and merging the two layers to incorporate it into
the models PDB file (You can do all of this in Swiss PDB). You could
try resubmitting this for modelling but I'm not really sure that it
would figure out what you were trying to do.
Let us know if you find a way to do this.
Simon.
--
Simon Andrews
Dept BNS
University of Newcastle upon Tyne
Tel +44 191 222 6000 ext 6596
s.r.andrews at ncl.ac.uk
