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1mf4

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[[Image:1mf4.jpg|left|200px]]
 
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==Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution==
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The line below this paragraph, containing "STRUCTURE_1mf4", creates the "Structure Box" on the page.
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<StructureSection load='1mf4' size='340' side='right'caption='[[1mf4]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1mf4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MF4 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_1mf4| PDB=1mf4 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mf4 OCA], [https://pdbe.org/1mf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mf4 RCSB], [https://www.ebi.ac.uk/pdbsum/1mf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mf4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PA2A3_NAJSG PA2A3_NAJSG] PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mf/1mf4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mf4 ConSurf].
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<div style="clear:both"></div>
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'''Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution'''
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==See Also==
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*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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Phospholipase A(2) (PLA(2)) (E. C. 3.1.1.4) is a common enzyme in the two-way cascade mechanism leading to the production of proinflammatory compounds known as eicosanoids. The binding of phospholipase A(2) to the membrane surface and hydrolysis of phospholipids are thought to involve the formation of a hydrophobic channel into which a single substrate molecule diffuses before its cleavage. To regulate the production of proinflammatory compounds, a specific peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) for the group I PLA(2) enzymes has been designed and synthesized. PLA(2) was isolated from Indian cobra (Naja naja sagittifera) venom and purified to homogeneity. The binding studies indicated the K(i) value of 1.02 +/- 0.10 x 10(-8) M. The purified PLA(2) samples and the designed inhibitor VAFRS were cocrystallized. The crystal structure of the complex was determined and refined to 1.9 A resolution. The peptide binds to PLA(2) at the active site and fills the hydrophobic channel completely. However, its placement with respect to the channel is in the opposite direction as compared to those observed in group II PLA(2)'s. Furthermore, the predominant intermolecular interactions involve strong electrostatic interactions between the side chains of peptide Arg and Asp 49 of PLA(2) together with a number of van der Waals interactions with other residues. A good number of observed interactions between the peptide and the protein indicate the significance of a structure-based drug design approach. The novel factor in the present sequence of the peptide is related to the introduction of a positively charged residue at the C-terminal part of the peptide.
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[[Category: Large Structures]]
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==About this Structure==
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1MF4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MF4 OCA].
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==Reference==
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Design of specific peptide inhibitors for group I phospholipase A2: structure of a complex formed between phospholipase A2 from Naja naja sagittifera (group I) and a designed peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) at 1.9 A resolution reveals unique features., Singh RK, Vikram P, Makker J, Jabeen T, Sharma S, Dey S, Kaur P, Srinivasan A, Singh TP, Biochemistry. 2003 Oct 14;42(40):11701-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14529280 14529280]
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[[Category: Naja sagittifera]]
[[Category: Naja sagittifera]]
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[[Category: Single protein]]
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[[Category: Dey S]]
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[[Category: Dey, S.]]
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[[Category: Jabeen T]]
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[[Category: Jabeen, T.]]
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[[Category: Kaur P]]
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[[Category: Kaur, P.]]
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[[Category: Makker J]]
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[[Category: Makker, J.]]
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[[Category: Paramsivam M]]
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[[Category: Paramsivam, M.]]
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[[Category: Sharma S]]
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[[Category: Sharma, S.]]
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[[Category: Singh RK]]
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[[Category: Singh, R K.]]
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[[Category: Singh TP]]
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[[Category: Singh, T P.]]
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[[Category: Srinivasan A]]
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[[Category: Srinivasan, A.]]
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[[Category: Vikram P]]
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[[Category: Vikram, P.]]
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[[Category: Designed inhibitor]]
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[[Category: Naja naja sagittifera]]
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[[Category: Phospholipase a2]]
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[[Category: Structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 00:57:39 2008''
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Current revision

Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution

PDB ID 1mf4

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