1jq9
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1jq9 |SIZE=350|CAPTION= <scene name='initialview01'>1jq9</scene>, resolution 1.80Å | |PDB= 1jq9 |SIZE=350|CAPTION= <scene name='initialview01'>1jq9</scene>, resolution 1.80Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene> | + | |LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1cl5|1CL5]], [[1fb2|1FB2]], [[1fe7|1FE7]], [[1fv0|1FV0]], [[1jq8|1JQ8]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jq9 OCA], [http://www.ebi.ac.uk/pdbsum/1jq9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jq9 RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: Kaur, P.]] | [[Category: Kaur, P.]] | ||
[[Category: Singh, T P.]] | [[Category: Singh, T P.]] | ||
| - | [[Category: ACY]] | ||
[[Category: daboia russelli pulchella]] | [[Category: daboia russelli pulchella]] | ||
[[Category: designed peptide]] | [[Category: designed peptide]] | ||
| Line 36: | Line 38: | ||
[[Category: structure]] | [[Category: structure]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:37:25 2008'' |
Revision as of 18:37, 30 March 2008
| |||||||
| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Phospholipase A(2), with EC number 3.1.1.4 | ||||||
| Related: | 1CL5, 1FB2, 1FE7, 1FV0, 1JQ8
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution
Overview
Phospholipase A(2) is an important enzyme involved in the production of prostaglandins and their related compounds causing inflammatory disorders. Among the several peptides tested, the peptide Phe-Leu-Ser-Tyr-Lys (FLSYK) showed the highest inhibition. The dissociation constant (K(d)) for this peptide was calculated to be 3.57 +/- 0.05 x 10(-9) m. In order to further improve the degree of inhibition of phospholipase A(2), a complex between Russells viper snake venom phospholipase A(2) and a peptide inhibitor FLSYK was crystallized, and its structure was determined by crystallographic methods and refined to an R-factor of 0.205 at 1.8 A resolution. The structure contains two crystallographically independent molecules of phospholipase A(2) (molecules A and B) and a peptide molecule specifically bound to molecule A only. The two molecules formed an asymmetric dimer. The dimerization caused a modification in the binding site of molecule A. The overall conformations of molecules A and B were found to be generally similar except three regions i.e. the Trp-31-containing loop (residues 25-34), the beta-wing consisting of two antiparallel beta-strands (residues 74-85) and the C-terminal region (residues 119-133). Out of the above three, the most striking difference pertains to the conformation of Trp-31 in the two molecules. The orientation of Trp-31 in molecule A was suitable for the binding of FLSYK, while it disallowed the binding of peptide to molecule B. The structure of the complex clearly shows that the peptide is so placed in the binding site of molecule A that the side chain of its lysine residue interacted extensively with the enzyme and formed several hydrogen bonds in addition to a strong electrostatic interaction with critical Asp-49. The C-terminal carboxylic group of the peptide interacted with the catalytic residue His-48.
About this Structure
1JQ9 is a Single protein structure of sequence from Daboia russellii pulchella. Full crystallographic information is available from OCA.
Reference
Crystal structure of a complex formed between a snake venom phospholipase A(2) and a potent peptide inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 A resolution., Chandra V, Jasti J, Kaur P, Dey S, Perbandt M, Srinivasan A, Betzel Ch, Singh TP, J Biol Chem. 2002 Oct 25;277(43):41079-85. Epub 2002 Aug 16. PMID:12186870
Page seeded by OCA on Sun Mar 30 21:37:25 2008
