[BiO BB] how pdb ID is defined?

[Xue Li]

Hi Tao,

Thank  you very much for your reply. Yes, you are right. I also find
the following link saying:

 3 Policy regarding assignment of PDB IDs
Can a PDB ID be requested? Neither a single PDB IDs nor a range of PDB
IDs can be
requested. PDB ID codes are automatically assigned and do not have any meaning.
When are PDB IDs assigned? PDB IDs are automatically assigned by software when
the author has completed his/her deposition (i.e. the author has
filled out at least the
minimal information for deposition and has pressed the deposit &
confirmation buttons.)


http://www.wwpdb.org/documentation/wwPDB-B-20070529.pdf    page 9

Thank you,

Li

2008/5/27 Huang Tao <silkhuang at gmail.com>:
> 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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>> http://www.bioinformatics.org/mailman/listinfo/bbb
>>
>
>
>
> --
> 黄韬， Tao Huang
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>



-- 
Xue, Li
Bioinformatics and Computational Biology program @ ISU
Ames, IA 50010
515-450-7183