[BiO BB] Getting PDB id from Swissprot entry

[Iddo Friedberg]

The best thing for you to do would be to BLAST the SP sequence against 
PDB, and take the top hit.

HTH,

./I

Sourangshu Bhattacharya wrote:
> 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
>>>>  
>>>>
>>>
>>
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
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http://ffas.ljcrf.edu/~iddo