[Biopython] PDBid to Uniprot ID?

[Peter]

On Wed, Jun 24, 2009 at 11:04 PM, Nick Matzke <matzke at berkeley.edu> wrote:
>
> Hi all,
>
> I have succeeded in using the BioPython PDB parser to download a PDB file,
> parse the structure, etc.  But I am wondering if there is an easy way to retrieve
> the UniProt ID that corresponds to the structure?
>
> I.e., if the structure is 1QFC...
> http://www.pdb.org/pdb/explore/explore.do?structureId=1QFC
>
> ...the Uniprot ID is (click "Sequence" above): P29288
> http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1QFC
>
> I don't see a way to get this out of the current parser, so I guess I will schlep
> through the downloaded structure file for "UNP    P29288" unless someone
> has a better idea.

Well, I would at least look for a line starting "DBREF" and then search that
for the reference.

Right now the PDB header parsing is minimal, and even that was something
of an after thought - Eric has been looking at this stuff recently, but I image
he will be busy with his GSoC work at the moment. This could be handled
as another tiny incremental addition to parse_pdb_header.py - right now I
don't think it looks at the "DBREF" lines.

Peter