[BiO BB] Getting PDB id from Swissprot entry

Sourangshu Bhattacharya sourangshu at csa.iisc.ernet.in
Thu Jul 1 14:02:26 EDT 2004


Hi Iddo,

I was going through a paper which gave Swissprot references for some 
proteins pairs which have circular permutations.
I wanted to have a look at their structures.

It seems I am facing many of the bellow mentioned problems. Many a times 
I dont find one of the structures (even homologies).
Also, it seems Swissprot lists multiple chains (if present) in some 
order in one and in another order in the other which is detected as 
permutations.
Unfortunately it is difficult to detect the same with structure 
alignment within a chain.

Thank you very much for the info. It will help me a lot.
Regards,
Sourangshu.

Iddo Friedberg wrote:

> Hi,
>
> I do not know for which particular purpose you are looking for SP <--> 
> PDB mappings, but beware the following perils & pitfalls:
>
> 1) The SP <--> PDB mapping can be many-to-many.
>
> 1.1 )There may be several entries in PDB which correspond to a single 
> swissprot entry. This is because the same protein may have been 
> structurally solved by different groups at different times, solved 
> with different ligands, point mutated, and so forth. Be very careful 
> about point-mutations: they do not have the same sequence in PDB as in 
> SP.
>
> 1.2) At the same time, there may be several SP entries corresponding 
> to a single PDB entry. This may be due to SP redundancy (although 
> database curators are doing a fantastic job of keeping that down), 
> close homologs, or point mutations.
>
> 2) An SP amino-acid sequence is rarely the same as the PDB sequence. 
> Usually only part of a structure is solved. Gaps abound, because 
> crystallographers sometimes cannot see the loops. There are large 
> deletions, because there are bits which are not crystallizable, or, if 
> NMR, they are trying to keep the protein short.
>
> 3) There are many SP entries which do have an equivalent in PDB, but 
> it does not say so in DR or PDB. See also the "40%" comment below.
>
> Cheers,
>
> Iddo
>
>
>
> Sourangshu Bhattacharya wrote:
>
>> Hi Dan,
>> Thank you very much. I didn't know about MSD.
>>
>> There is also an entry HSSP in swissprot which gives homologues.
>>
>> Sourangshu
>>
>> Dan Bolser wrote:
>>
>>> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote:
>>>
>>>  
>>>
>>>> Hi,
>>>>
>>>> Is there a direct way (without reading the protein name from 
>>>> swissprot and searching in PDB) of getting the PDB id of the 
>>>> protein corresponding to a particular Swissprot id ?
>>>>   
>>>
>>>
>>>
>>> I would use the MSD database, which maintains a manually curated 
>>> version
>>> of the SwissProt to PDB mapping.
>>>
>>>  
>>>
>>>> Also, how do I know whether structure for a particular protein 
>>>> corresponding to a swissprot id has been determined or not ?
>>>>   
>>>
>>>
>>>
>>> Strictly speeking, the above mapping gives you this. More 
>>> realistically,
>>> however, you can consider very close homologues to the above set as 
>>> also
>>> 'solved'. Where you draw the line is a matter of requirement, but 
>>> you can
>>> get reasonable models (allegedly) at > 40% sequence identity, or
>>> reasonable 'fold prediction' at much larger distances (see 
>>> SUPERFAMILY for
>>> example).
>>>
>>> It all depends on what you want to do.
>>>
>>>  
>>>
>>>> Thank you very much..
>>>>
>>>> Regards,
>>>> Sourangshu.
>>>>
>>>>
>>>>   
>>>
>>>
>>>
>>> _______________________________________________
>>> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>  
>>>
>>
>

-- 

Sourangshu Bhattacharya
PhD Student,
Dept. of Computer Science & Automation,
Indian Institute of Science, 
Bangalore - 560012, India.

Website: http://people.csa.iisc.ernet.in/sourangshu
Cell Phone : 91-98457 97492




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