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1dpy

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[[Image:1dpy.gif|left|200px]]
 
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{{Structure
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==THREE-DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 A RESOLUTION==
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|PDB= 1dpy |SIZE=350|CAPTION= <scene name='initialview01'>1dpy</scene>, resolution 2.45&Aring;
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<StructureSection load='1dpy' size='340' side='right'caption='[[1dpy]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
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<table><tr><td colspan='2'>[[1dpy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bungarus_caeruleus Bungarus caeruleus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DPY FirstGlance]. <br>
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|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]
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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]] 2.45&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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}}
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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=1dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dpy OCA], [https://pdbe.org/1dpy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dpy RCSB], [https://www.ebi.ac.uk/pdbsum/1dpy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dpy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PA2B_BUNCE PA2B_BUNCE]
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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/dp/1dpy_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=1dpy ConSurf].
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<div style="clear:both"></div>
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'''THREE-DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 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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This is the first phospholipase A2 (PLA2) structure from the family of kraits. The protein was isolated from Bungarus caeruleus (common krait) and the primary sequence was determined using cDNA approach. Three-dimensional structure of this presynaptic neurotoxic PLA2 from group I has been determined by molecular replacement method using the model of PLA2 component of beta2-bungarotoxin (Bungarus multicinctus) and refined using CNS package to a final R-factor of 20.1 % for all the data in resolution range 20.0-2.4 A. The final refined model comprises 897 protein atoms and 77 water molecules. The overall framework of krait phospholipase A2 with three long helices and two short antiparallel beta-strands is extremely similar to those observed for other group I PLA2s. However, the critical parts of PLA2 folding are concerned with its various functional loops. The conformations of these loops determine the efficiency of enzyme action and presence/absence of various pharmacological functions. In the present structure calcium-binding loop is occupied by a sodium ion with a 7-fold co-ordination. The conformation of loop 55-75 in krait PLA2 corresponds to a very high activity of the enzyme. A comparison of its sequence with multimeric PLA2s clearly shows the absence of critical residues such as Tyr3, Trp61 and Phe64, which are involved in the multimerization of PLA2 molecules. The protein shows anticoagulant and neurotoxic activities.
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==About this Structure==
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1DPY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bungarus_caeruleus Bungarus caeruleus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DPY OCA].
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==Reference==
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Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites., Singh G, Gourinath S, Sharma S, Paramasivam M, Srinivasan A, Singh TP, J Mol Biol. 2001 Apr 6;307(4):1049-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11286555 11286555]
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[[Category: Bungarus caeruleus]]
[[Category: Bungarus caeruleus]]
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[[Category: Phospholipase A(2)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Gourinath S]]
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[[Category: Gourinath, S.]]
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[[Category: Paramasivam M]]
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[[Category: Paramasivam, M.]]
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[[Category: Sharma S]]
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[[Category: Sharma, S.]]
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[[Category: Singh G]]
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[[Category: Singh, G.]]
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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: NA]]
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[[Category: crystal structure]]
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[[Category: indian common krait venom]]
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[[Category: phospholipase a2]]
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[[Category: refinement]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:42:24 2008''
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Current revision

THREE-DIMENSIONAL STRUCTURE OF A NOVEL PHOSPHOLIPASE A2 FROM INDIAN COMMON KRAIT AT 2.45 A RESOLUTION

PDB ID 1dpy

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