2qvd: Difference between revisions

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-[[Image:2qvd.png|left|200px]]
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+==Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution==
-The line below this paragraph, containing "STRUCTURE_2qvd", creates the "Structure Box" on the page.
+<StructureSection load='2qvd' size='340' side='right'caption='[[2qvd]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2qvd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Daboia_russelii_pulchella Daboia russelii pulchella]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BER:BERBERINE'>BER</scene></td></tr>
-{{STRUCTURE_2qvd|  PDB=2qvd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvd OCA], [https://pdbe.org/2qvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvd RCSB], [https://www.ebi.ac.uk/pdbsum/2qvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/2qvd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2qvd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal of Russell Viper venom phospholipase A(2) complexed with an isoquinoline alkaloid, berberine from a herbaceous plant Cardiospermum halicacabum, was prepared and its structure was solved by X-ray crystallography. The crystal diffracted up to 1.93A and the structure solution clearly located the position of berberine in the active site of the enzyme. Two hydrogen bonds, one direct and the other water mediated, were formed between berberine and the enzyme. Gly 30 and His 48 made these two hydrogen bonds. Additionally, the hydrophobic surface of berberine made a number of hydrophobic contacts with side chains of neighboring amino acids. Surface Plasmon Resonance studies revealed strong binding affinity between berberine and phospholipase A(2). Enzyme inhibition studies proved that berberine is a competitive inhibitor of phospholipase A(2). It was inferred that the isoquinoline alkaloid, berberine, is a potent natural inhibitor of phospholipaseA(2).
-===Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution===
+Identification of a novel and potent inhibitor of phospholipase A(2) in a medicinal plant: crystal structure at 1.93A and Surface Plasmon Resonance analysis of phospholipase A(2) complexed with berberine.,Chandra DN, Prasanth GK, Singh N, Kumar S, Jithesh O, Sadasivan C, Sharma S, Singh TP, Haridas M Biochim Biophys Acta. 2011 May;1814(5):657-63. Epub 2011 Mar 17. PMID:21420512<ref>PMID:21420512</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_21420512}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2qvd" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21420512 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_21420512}}
-==About this Structure==
-[[2qvd]] is a 1 chain structure of [[Phospholipase A2]] with sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVD OCA].
 ==See Also==
-*[[Phospholipase A2]]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:021420512</ref><references group="xtra"/>
+__TOC__
-[[Category: Daboia russellii pulchella]]
+</StructureSection>
-[[Category: Chandra, D N.]]
+[[Category: Daboia russelii pulchella]]
-[[Category: Haridas, M.]]
+[[Category: Large Structures]]
-[[Category: Jithesh, O.]]
+[[Category: Chandra DN]]
-[[Category: Kumar, S.]]
+[[Category: Haridas M]]
-[[Category: Sharma, S.]]
+[[Category: Jithesh O]]
-[[Category: Singh, N.]]
+[[Category: Kumar S]]
-[[Category: Singh, T P.]]
+[[Category: Sharma S]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
+[[Category: Singh N]]
-[[Category: Hydrolysis]]
+[[Category: Singh TP]]
-[[Category: Inhibitor]]
-[[Category: Lipid degradation]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Neurotoxin]]
-[[Category: Phospholipid]]
-[[Category: Plant extraxt]]
-[[Category: Presynaptic neurotoxin]]
-[[Category: Secreted]]
-[[Category: Toxin]]