[BiO BB] how pdb ID is defined?

[Huang Tao]

About PDB ID, please refer to:
http://www.rcsb.org/robohelp/search_database/pdb_identifier.htm.

Usually, you will find the last three characters is an abbreviation of
certain protein name. For example, there is an entry of ubiquitin of which
PDB ID is 1UBQ.  However, you should not determine *biological distance
merely based on their pdb IDs*. It's possible, but not absolutely right.

You may use sequence alignment tools (e.g. ClustalW) to determine the
biological distance between your interested proteins, or use "Sequence
Search (http://www.rcsb.org/pdb/search/searchSequence.do)"  provided by RCSB
PDB to find similar proteins, actually, it is a BLAST service.


Cheers,

Tao

2008/5/27 Xue Li <me.lixue at gmail.com>:

> 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?
>
> Thanks a lot.
>
> --
> Xue, Li
> Bioinformatics and Computational Biology program @ ISU
> Ames, IA 50010
> 515-450-7183
>
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>



-- 
黄韬， Tao Huang