2ody: Difference between revisions

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 ==Thrombin-bound boophilin displays a functional and accessible reactive-site loop==
-<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+<StructureSection load='2ody' size='340' side='right'caption='[[2ody]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ody]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Boophilus_microplus Boophilus microplus] and [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ODY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ODY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ody]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Rhipicephalus_microplus Rhipicephalus microplus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ODY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ODY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ody FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ody OCA], [http://pdbe.org/2ody PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ody RCSB], [http://www.ebi.ac.uk/pdbsum/2ody PDBsum]</span></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=2ody FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ody OCA], [https://pdbe.org/2ody PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ody RCSB], [https://www.ebi.ac.uk/pdbsum/2ody PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ody ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/THRB_BOVIN THRB_BOVIN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing (By similarity). [[http://www.uniprot.org/uniprot/BOOH2_BOOMI BOOH2_BOOMI]] Prevents blood clot formation to allow successful feeding and digestion through its inhibition activity of thrombin and other host anticoagulating factors like kallikrein, coagulation factor VII, or plasmin.<ref>PMID:18286181</ref>
+[https://www.uniprot.org/uniprot/THRB_BOVIN THRB_BOVIN] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing (By similarity).
 == 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/od/2ody_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/2ody_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2ody ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Thrombin|Thrombin]]
+*[[Thrombin 3D Structures|Thrombin 3D Structures]]
+*[[Thrombin heavy chain|Thrombin heavy chain]]
+*[[Thrombin light chain|Thrombin light chain]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Boophilus microplus]]
 [[Category: Bos taurus]]
-[[Category: Thrombin]]
+[[Category: Large Structures]]
-[[Category: Fuentes-Prior, P]]
+[[Category: Rhipicephalus microplus]]
-[[Category: Macedo-Ribeiro, S]]
+[[Category: Fuentes-Prior P]]
-[[Category: Pereira, P J.B]]
+[[Category: Macedo-Ribeiro S]]
-[[Category: Blood clotting-blood clotting inhibitor complex]]
+[[Category: Pereira PJB]]
-[[Category: Kunitz-type thrombin inhibitor]]