1vl9: Difference between revisions

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-[[Image:1vl9.png|left|200px]]
-{{STRUCTURE_1vl9|  PDB=1vl9  |  SCENE=  }}
+==Atomic resolution (0.97A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2==
+<StructureSection load='1vl9' size='340' side='right'caption='[[1vl9]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vl9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VL9 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.97&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vl9 OCA], [https://pdbe.org/1vl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vl9 RCSB], [https://www.ebi.ac.uk/pdbsum/1vl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vl9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA21B_BOVIN PA21B_BOVIN] PA2 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/vl/1vl9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1vl9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme phospholipase A2 catalyzes the hydrolysis of the sn-2 acyl chain of phospholipids, forming fatty acids and lysophospholipids. The crystal structure of a triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 in which the lysine residues at positions 53, 56 and 121 are replaced recombinantly by methionines has been determined at atomic resolution (0.97 A). The crystal is monoclinic (space group P2), with unit-cell parameters a = 36.934, b = 23.863, c = 65.931 A, beta = 101.47 degrees. The structure was solved by molecular replacement and has been refined to a final R factor of 10.6% (Rfree = 13.4%) using 63,926 unique reflections. The final protein model consists of 123 amino-acid residues, two calcium ions, one chloride ion, 243 water molecules and six 2-methyl-2,4-pentanediol molecules. The surface-loop residues 60-70 are ordered and have clear electron density.
-===Atomic resolution (0.97A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2===
+Atomic resolution (0.97 A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2.,Sekar K, Rajakannan V, Gayathri D, Velmurugan D, Poi MJ, Dauter M, Dauter Z, Tsai MD Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jan 1;61(Pt 1):3-7., Epub 2004 Sep 25. PMID:16508077<ref>PMID:16508077</ref>
-{{ABSTRACT_PUBMED_16508077}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1vl9" style="background-color:#fffaf0;"></div>
-[[1vl9]] is a 1 chain structure of [[Phospholipase A2]] with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VL9 OCA].
 ==See Also==
-*[[Phospholipase A2|Phospholipase A2]]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016508077</ref><ref group="xtra">PMID:018754631</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Dauter, M.]]
+[[Category: Large Structures]]
-[[Category: Dauter, Z.]]
+[[Category: Dauter M]]
-[[Category: Gayathri, D.]]
+[[Category: Dauter Z]]
-[[Category: Poi, M J.]]
+[[Category: Gayathri D]]
-[[Category: Rajakannan, V.]]
+[[Category: Poi M-J]]
-[[Category: Sekar, K.]]
+[[Category: Rajakannan V]]
-[[Category: Tsai, M D.]]
+[[Category: Sekar K]]
-[[Category: Velmurugan, D.]]
+[[Category: Tsai M-D]]
-[[Category: Alpha helix]]
+[[Category: Velmurugan D]]
-[[Category: Beta sheet]]
-[[Category: Calcium ion]]
-[[Category: Hydrolase]]
-[[Category: Triple mutant]]