[BiO BB] Getting PDB id from Swissprot entry
Iddo Friedberg
idoerg at burnham.org
Thu Jul 1 14:15:07 EDT 2004
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
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
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