2dw1: Difference between revisions

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-{{Seed}}
-[[Image:2dw1.png|left|200px]]
-<!--
+==Crystal structure of VAP2 from Crotalus atrox venom (Form 2-2 crystal)==
-The line below this paragraph, containing "STRUCTURE_2dw1", creates the "Structure Box" on the page.
+<StructureSection load='2dw1' size='340' side='right'caption='[[2dw1]], [[Resolution|resolution]] 2.50&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'>[[2dw1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Crotalus_atrox Crotalus atrox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DW1 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GM6:3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE'>GM6</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2dw1|  PDB=2dw1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw1 OCA], [https://pdbe.org/2dw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dw1 RCSB], [https://www.ebi.ac.uk/pdbsum/2dw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VM3VB_CROAT VM3VB_CROAT] Zinc metalloproteinase-disintegrin-like VAP2B: zinc metalloprotease that abolishes platelet aggregation induced by collagen, but has no effect on platelet aggregation induced by ADP or thromboxane analog. This inhibition may be due to its ability to bind collagen and block the binding site on collagen for platelets and/or to its ability to bind to the platelet alpha-2/beta-1 collagen receptor (ITGA2/ITGB1) to block its interaction with collagen and hence prevent platelet stimulation.  Disintegrin catrocollastatin-C: abolishes platelet aggregation induced by collagen (IC(50)=66 nM) but not ADP-stimulated platelet aggregation. This inhibition may be due to its ability to bind collagen and block the binding site on collagen for platelets and/or to its ability to bind to the platelet alpha-2/beta-1 collagen receptor (ITGA2/ITGB1) to block its interaction with collagen and hence prevent platelet stimulation.
+== 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/dw/2dw1_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=2dw1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Catrocollastatin/vascular apoptosis-inducing protein (VAP)2B is a metalloproteinase from Crotalus atrox venom, possessing metalloproteinase/disintegrin/cysteine-rich (MDC) domains that bear the typical domain architecture of a disintegrin and metalloproteinase (ADAM)/adamalysin/reprolysin family proteins. Here we describe crystal structures of catrocollastatin/VAP2B in three different crystal forms, representing the first reported crystal structures of a member of the monomeric class of this family of proteins. The overall structures show good agreement with both monomers of atypical homodimeric VAP1. Comparison of the six catrocollastatin/VAP2B monomer structures and the structures of VAP1 reveals a dynamic, modular architecture that may be important for the functions of ADAM/adamalysin/reprolysin family proteins.
-===Crystal structure of VAP2 from Crotalus atrox venom (Form 2-2 crystal)===
+Crystal structures of catrocollastatin/VAP2B reveal a dynamic, modular architecture of ADAM/adamalysin/reprolysin family proteins.,Igarashi T, Araki S, Mori H, Takeda S FEBS Lett. 2007 May 29;581(13):2416-22. Epub 2007 Apr 30. PMID:17485084<ref>PMID:17485084</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dw1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17485084}}, adds the Publication Abstract to the page
+*[[Disintegrin|Disintegrin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17485084 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17485084}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DW1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Crotalus_atrox Crotalus atrox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW1 OCA].
-==Reference==
-Crystal structures of catrocollastatin/VAP2B reveal a dynamic, modular architecture of ADAM/adamalysin/reprolysin family proteins., Igarashi T, Araki S, Mori H, Takeda S, FEBS Lett. 2007 May 29;581(13):2416-22. Epub 2007 Apr 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17485084 17485084]
-Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom., Igarashi T, Oishi Y, Araki S, Mori H, Takeda S, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jul 1;62(Pt, 7):688-91. Epub 2006 Jun 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16820695 16820695]
-Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold., Takeda S, Igarashi T, Mori H, Araki S, EMBO J. 2006 Jun 7;25(11):2388-96. Epub 2006 May 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16688218 16688218]
-cDNA cloning and some additional peptide characterization of a single-chain vascular apoptosis-inducing protein, VAP2., Masuda S, Maeda H, Miao JY, Hayashi H, Araki S, Endothelium. 2007 Mar-Apr;14(2):89-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17497365 17497365]
-Two vascular apoptosis-inducing proteins from snake venom are members of the metalloprotease/disintegrin family., Masuda S, Hayashi H, Araki S, Eur J Biochem. 1998 Apr 1;253(1):36-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9578458 9578458]
 [[Category: Crotalus atrox]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Araki, S.]]
+[[Category: Araki S]]
-[[Category: Igarashi, T.]]
+[[Category: Igarashi T]]
-[[Category: Takeda, S.]]
+[[Category: Takeda S]]
-[[Category: Apoptotic toxin]]
-[[Category: Metalloproteinase]]
-[[Category: Svmp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 21:14:12 2008''