[BiO BB] Getting PDB id from Swissprot entry

[Sourangshu Bhattacharya]

Hi Peter,
Actually I am not working with the Swissprot database files, but only 
with the web interface.

Thank you,
Sourangshu

Peter Rice wrote:

> 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 ?
>
>
> Yes ... SwissProt has a DR (database reference) line that points to 
> the PDB entry (assuming, or course, that there is a solved structure 
> in PDB for that protein).
>
> For example, this entry has 3 PDB references.
>
> ID   AMIC_PSEAE     STANDARD;      PRT;   384 AA.
> AC   P27017;
> DT   01-AUG-1992 (Rel. 23, Created)
> DT   16-OCT-2001 (Rel. 40, Last sequence update)
> DT   15-JUN-2004 (Rel. 44, Last annotation update)
> DE   Aliphatic amidase expression-regulating protein.
> GN   AMIC OR PA3364.
> OS   Pseudomonas aeruginosa.
> OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
> OC   Pseudomonadaceae; Pseudomonas.
>
> ..... reference (citation) section skipped .....
>
>
> CC   -!- FUNCTION: Negatively regulates the expression of the aliphatic
> CC       amidase operon. AmiC functions by inhibiting the action of 
> amiR at
> CC       the protein level. It exhibits protein kinase activity.
> CC   -!- SUBUNIT: Homodimer. Forms a complex with amiR.
> CC   -!- DOMAIN: Consists of two beta-alpha-beta domains with a central
> CC       cleft in which the amide binds.
> CC 
> -------------------------------------------------------------------------- 
>
> CC   This SWISS-PROT entry is copyright. It is produced through a 
> collaboration
> CC   between  the Swiss Institute of Bioinformatics  and the  EMBL 
> outstation -
> CC   the European Bioinformatics Institute.  There are no  
> restrictions on  its
> CC   use  by  non-profit  institutions as long  as its content  is  in 
> no  way
> CC   modified and this statement is not removed.  Usage  by  and for 
> commercial
> CC   entities requires a license agreement (See 
> http://www.isb-sib.ch/announce/
> CC   or send an email to license at isb-sib.ch).
> CC 
> -------------------------------------------------------------------------- 
>
> DR   EMBL; X13776; CAA32024.1; -.
> DR   EMBL; AE004758; AAG06752.1; -.
> DR   PIR; C83226; C83226.
> DR   PDB; 1PEA; 03-APR-96.
> DR   PDB; 1QNL; 23-DEC-99.
> DR   PDB; 1QO0; 23-DEC-99.
> DR   InterPro; IPR000709; Leu_Ile_Val_bind.
> DR   PRINTS; PR00337; LEUILEVALBP.
> KW   Transferase; Kinase; Repressor; 3D-structure; Complete proteome;
> KW   Direct protein sequencing.
>
> ..... features and sequence skipped .....
>
> Hope that helps,
>
> Peter Rice
>
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-- 

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