[BiO BB] how pdb ID is defined?

[Dan Bolser]

2008/6/14 Bour, Stephan (NIH/NHLBI) [E] <sbour at nhlbi.nih.gov>:
> 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.
> http://david.abcc.ncifcrf.gov/

How do you mean?

> Stephan.
>
>
> -----Original Message-----
> 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:
> http://pdbwiki.org/index.php/PDB_code
>
> Which is part of the PDB FAQ that is collaboratively maintained there:
> http://pdbwiki.org/index.php/PDB_FAQ
>
> HTH,
>
> Dan.
>
>
>>
>> Thanks a lot.
>>
>> --
>> Xue, Li
>> Bioinformatics and Computational Biology program @ ISU
>> Ames, IA 50010
>> 515-450-7183
>>
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>
>
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