2dm6
From Proteopedia
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|PDB= 2dm6 |SIZE=350|CAPTION= <scene name='initialview01'>2dm6</scene>, resolution 2.000Å | |PDB= 2dm6 |SIZE=350|CAPTION= <scene name='initialview01'>2dm6</scene>, resolution 2.000Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=IMN:INDOMETHACIN'>IMN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1v3v|1V3V]], [[1v3t|1V3T]], [[1v3u|1V3U]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dm6 OCA], [http://www.ebi.ac.uk/pdbsum/2dm6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dm6 RCSB]</span> | ||
}} | }} | ||
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[[Category: Shimizu, T.]] | [[Category: Shimizu, T.]] | ||
[[Category: Yokomizo, T.]] | [[Category: Yokomizo, T.]] | ||
| - | [[Category: IMN]] | ||
| - | [[Category: NAP]] | ||
| - | [[Category: TAM]] | ||
[[Category: nad(p)-binding rossmann-fold domain]] | [[Category: nad(p)-binding rossmann-fold domain]] | ||
[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
| Line 37: | Line 37: | ||
[[Category: structural genomic]] | [[Category: structural genomic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:36:29 2008'' |
Revision as of 23:36, 30 March 2008
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| , resolution 2.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Related: | 1V3V, 1V3T, 1V3U
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex
Overview
The crystal structure of the ternary complex of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin (15-oxo-PG) 13-reductase (LTB4 12HD/PGR), an essential enzyme for eicosanoid inactivation pathways, with indomethacin and NADP+ has been solved. An indomethacin molecule bound in the anti-configuration at one of the two active site clefts of the homo-dimer interface in the LTB4 12HD/PGR and was confirmed by a binding calorimetry. The chlorobenzene ring is buried in the hydrophobic pore used as a binding site by the omega-chain of 15-oxo-PGE2. The carboxyl group interacts with the guanidino group of Arg56 and the phenolic hydroxyl group of Tyr262. Indomethacin shows a broad spectrum of efficacy against lipid-mediator related proteins including cyclooxygenase-2, phospholipase A2, PGF synthase and PGE synthase-2 but in the syn-configuration as well as LTB4 12HD/PGR in the anti-configuration. Indomethacin does not necessarily mimic the binding mode of the lipid-mediator substrates in the active sites of these complex structures. Thus, the broad spectrum of indomethacin efficacy can be attributed to its ability to adopt a range of different stable conformations. This allows the indomethacin to adapt to the distinct binding site features of each protein whilst maintaining favorable interactions between the carboxyl group and a counter charged functional group.
About this Structure
2DM6 is a Single protein structure of sequence from Cavia porcellus. Full crystallographic information is available from OCA.
Reference
Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex reveals the structural basis of broad spectrum indomethacin efficacy., Hori T, Ishijima J, Yokomizo T, Ago H, Shimizu T, Miyano M, J Biochem. 2006 Sep;140(3):457-66. Epub 2006 Aug 17. PMID:16916844
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