[BiO BB] how pdb ID is defined?
Bour, Stephan (NIH/NHLBI) [E]
sbour at nhlbi.nih.gov
Sat Jun 14 09:50:56 EDT 2008
You may want to check out the DAVID set of tools from the National Institute of Allergy and Infectious Diseases. It was originally designed to address this kind of issue.
From: Dan Bolser [mailto:dan.bolser at gmail.com]
Sent: Sat 6/14/2008 9:42 AM
To: General Forum at Bioinformatics.Org
Subject: Re: [BiO BB] how pdb ID is defined?
On 27/05/2008, Xue Li <me.lixue at gmail.com> wrote:
> Dear all,
> Maybe this is a naive question. I just noticed that proteins 2GSA and
> 4GSA have similar name and denote almost the same protein.
> 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE
> (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE
> 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE
> AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM)
> Also, 2ae2 and 1ae1 denote similar proteins.
> 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE
> 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP
> Would someone please tell me how PDB ID is defined? Given a list of
> pdb ID, can I find biological distance merely based on their pdb IDs?
In 'the old days' PDB ID's were chosen by the author, and 'updated'
versions of the same protein were indexed by their first digit.. i.e.
1sod / 2sod / etc. for the SuperOxide Dismutase structures.
These days the id is arbitrary as you discovered.
There is a page dealing with this question on PDBWiki:
Which is part of the PDB FAQ that is collaboratively maintained there:
> Thanks a lot.
> Xue, Li
> Bioinformatics and Computational Biology program @ ISU
> Ames, IA 50010
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