[BiO BB] Getting PDB id from Swissprot entry

Peter Rice pmr at ebi.ac.uk
Thu Jul 1 08:27:09 EDT 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 ?

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   This SWISS-PROT entry is copyright. It is produced through a 
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 
CC   entities requires a license agreement (See 
CC   or send an email to license at isb-sib.ch).
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.
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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