[BiO BB] Getting PDB id from Swissprot entry

D. Norris dmnunif at charter.net
Thu Jul 1 22:58:05 EDT 2004


You will never really contribute much until you remember that a biological
system far exceeds lists of genes and proteins, i.e., parts lists.

dmn
----- Original Message ----- 
From: "Iddo Friedberg" <idoerg at burnham.org>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Thursday, July 01, 2004 1:15 PM
Subject: Re: [BiO BB] Getting PDB id from Swissprot entry


>
>
> 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
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board





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