1fdk
From Proteopedia
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|PDB= 1fdk |SIZE=350|CAPTION= <scene name='initialview01'>1fdk</scene>, resolution 1.91Å | |PDB= 1fdk |SIZE=350|CAPTION= <scene name='initialview01'>1fdk</scene>, resolution 1.91Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLE:1-DECYL-3-TRIFLUORO+ETHYL-SN-GLYCERO-2-PHOSPHOMETHANOL'>GLE</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= MATURE PLA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus]) | |GENE= MATURE PLA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fdk OCA], [http://www.ebi.ac.uk/pdbsum/1fdk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fdk RCSB]</span> | ||
}} | }} | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: GLE]] | ||
[[Category: carboxylic ester hydrolase]] | [[Category: carboxylic ester hydrolase]] | ||
[[Category: enzyme]] | [[Category: enzyme]] | ||
[[Category: lipid degradation]] | [[Category: lipid degradation]] | ||
| - | ''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 20:20:46 2008'' |
Revision as of 17:20, 30 March 2008
| |||||||
| , resolution 1.91Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | MATURE PLA2 (Bos taurus) | ||||||
| Activity: | Phospholipase A(2), with EC number 3.1.1.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)
Overview
The structure of recombinant bovine pancreatic phospholipase A2 (PLA2) complexed with the competitive inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero -2-phosphomethanol (hereafter MJ33), a phospholipid analogue without the sn-3 phosphodiester group, has been determined. The crystals are trigonal, space group P3121, a = b = 46.36 A and c = 102.56 A, and isomorphous to the recombinant PLA2 with one molecule in the asymmetric unit. The structure was refined using 8082 reflections between 8.0 and 1.91 A resolution to a final R-value of 18.4% [Rfree = 28.0%]. The model includes 957 protein atoms, 86 water molecules, one calcium ion, and 26 non-hydrogen atoms of the inhibitor MJ33. The overall tertiary fold of the complex is very similar to that of the inhibitor-free recombinant PLA2 with a root mean square deviation of 0.32 A for all the backbone atoms. The electron density of the surface loop residues 62-66 is clear and ordered, unlike the other trigonal bovine PLA2 structures done to date. This structural change could be responsible for the interfacial allosteric activation, which thermodynamically relates the enhanced binding of the substrate mimic to the active site of the enzyme. MJ33 is tightly bound in the active-site cleft, dislodging the equatorial coordinated calcium water (W5), the putative catalytic water W6, and the neighboring water W7. The axial coordinated calcium water is missing; thus the hexacoordinated calcium is a monocapped pentagonal pyramid. Although MJ33 is a sn-2 tetrahedral mimic, its phosphate binds to PLA2 differently from the sn-2 phosphonate analogue of phospholipids, another tetrahedral mimic. The knowledge of the active-site geometry of MJ33 would be useful in the design of more useful therapeutic agents for PLA2.
About this Structure
1FDK is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
Reference
Crystal structure of the complex of bovine pancreatic phospholipase A2 with the inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero-2-phosphomethanol,., Sekar K, Eswaramoorthy S, Jain MK, Sundaralingam M, Biochemistry. 1997 Nov 18;36(46):14186-91. PMID:9369492
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