1m8t: Difference between revisions

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-{{Seed}}
-[[Image:1m8t.png|left|200px]]
-<!--
+==Structure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form==
-The line below this paragraph, containing "STRUCTURE_1m8t", creates the "Structure Box" on the page.
+<StructureSection load='1m8t' size='340' side='right'caption='[[1m8t]], [[Resolution|resolution]] 2.10&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'>[[1m8t]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ophiophagus_hannah Ophiophagus hannah]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M8T 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>
-{{STRUCTURE_1m8t|  PDB=1m8t  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m8t OCA], [https://pdbe.org/1m8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m8t RCSB], [https://www.ebi.ac.uk/pdbsum/1m8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m8t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2A2_OPHHA PA2A2_OPHHA] Snake venom phospholipase A2 (PLA2) that displays edema-inducing and moderate anticoagulant activities. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
+== 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/m8/1m8t_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=1m8t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An acidic PLA(2) (OH APLA(2)-II) from the venom of Ophiophagus hannah (king cobra) shows greater phospholipase A(2) activity and weaker cardiotoxic and myotoxic activity than a homologous acidic PLA(2) from the same venom. The crystal of the enzyme belongs to space group P6(3). The crystals are invariably hemihedrally twinned, exhibiting perfect 622 Laue symmetry. The structure was determined by molecular replacement and refined using a hemihedral twinning program at 2.1 A resolution. The final model has reasonable stereochemistry and a crystallographic R factor of 19.5% (R(free) = 21.5%). The structure reveals the molecular arrangement and the mode of twinning. There are six independent molecules in the asymmetric unit. Owing to the presence of a non-crystallographic twofold parallel to the hemihedral twinning twofold, the molecular packing in the twinned crystal is extremely similar to that in an untwinned crystal for four of the molecules. This unique molecular arrangement may be related to the difficulty in recognizing the twinning. The structure was compared with the previously determined structure of a homologous acidic PLA(2) from the same source. The comparison shows structural changes that might be implicated in the increased catalytic activity and weakened toxicity.
-===Structure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form===
+Structure of a king cobra phospholipase A2 determined from a hemihedrally twinned crystal.,Xu S, Gu L, Wang Q, Shu Y, Song S, Lin Z Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1574-81. Epub 2003, Aug 19. PMID:12925787<ref>PMID:12925787</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1m8t" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12925787}}, adds the Publication Abstract to the page
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12925787 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12925787}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-M8T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Ophiophagus_hannah Ophiophagus hannah]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M8T OCA].
-==Reference==
-Structure of a king cobra phospholipase A2 determined from a hemihedrally twinned crystal., Xu S, Gu L, Wang Q, Shu Y, Song S, Lin Z, Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1574-81. Epub 2003, Aug 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12925787 12925787]
 [[Category: Ophiophagus hannah]]
-[[Category: Single protein]]
+[[Category: Gu L]]
-[[Category: Gu, L.]]
+[[Category: Lin Z]]
-[[Category: Lin, Z.]]
+[[Category: Shu Y]]
-[[Category: Shu, Y.]]
+[[Category: Wang Q]]
-[[Category: Wang, Q.]]
+[[Category: Xu S]]
-[[Category: Xu, S.]]
-[[Category: Alpha]]
-[[Category: Beta]]
-[[Category: Phospholipase a2 structure]]
-[[Category: Twinned crystal]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 23:27:39 2008''