2ody - Revision history

OCA at 10:36, 30 August 2023

2023-08-30T10:36:15Z

←Older revision		Revision as of 10:36, 30 August 2023
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	<StructureSection load='2ody' size='340' side='right'caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2ody' size='340' side='right'caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ody]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Boophilus_microplus Boophilus microplus~~] and [https://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 [https://proteopedia.org/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" 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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.35Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [https://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'>[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>		<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>		</table>
	== Function ==		== Function ==
-	[[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). [[https://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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Boophilus microplus]]
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thrombin~~]]	+	[[Category: Rhipicephalus microplus]]
-	[[Category: Fuentes-Prior, P]]	+	[[Category: Fuentes-Prior P]]
-	[[Category: Macedo-Ribeiro, S]]	+	[[Category: Macedo-Ribeiro S]]
-	[[Category: Pereira~~, P J.B]]~~	+	[[Category: Pereira PJB]]
-	~~[[Category: Blood clotting-blood clotting inhibitor complex]]~~	+
-	~~[[Category: Kunitz-type thrombin inhibitor~~]]	+

OCA at 07:50, 2 March 2022

2022-03-02T07:50:52Z

←Older revision		Revision as of 07:50, 2 March 2022
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	<StructureSection load='2ody' size='340' side='right'caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2ody' size='340' side='right'caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== 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~~://proteopedia.org/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/Boophilus_microplus Boophilus microplus] and [https://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 [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" 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>		</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='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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/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], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ody ProSAT]</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>		</table>
	== Function ==		== 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). [[https://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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:59, 27 May 2020

2020-05-27T07:59:45Z

←Older revision		Revision as of 07:59, 27 May 2020
Line 1:		Line 1:

	==Thrombin-bound boophilin displays a functional and accessible reactive-site loop==		==Thrombin-bound boophilin displays a functional and accessible reactive-site loop==
-	<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='2ody' size='340' side='right'caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== 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 [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://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='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='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='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='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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ody ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ody ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Thrombin\|Thrombin]]	+	*[[Thrombin 3D Structures\|Thrombin 3D Structures]]
	*[[Thrombin heavy chain\|Thrombin heavy chain]]		*[[Thrombin heavy chain\|Thrombin heavy chain]]
	*[[Thrombin light chain\|Thrombin light chain]]		*[[Thrombin light chain\|Thrombin light chain]]
Line 40:		Line 40:
	[[Category: Boophilus microplus]]		[[Category: Boophilus microplus]]
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
		+	[[Category: Large Structures]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
	[[Category: Fuentes-Prior, P]]		[[Category: Fuentes-Prior, P]]

OCA at 07:05, 22 August 2018

2018-08-22T07:05:26Z

←Older revision		Revision as of 07:05, 22 August 2018
Line 1:		Line 1:
		+
	==Thrombin-bound boophilin displays a functional and accessible reactive-site loop==		==Thrombin-bound boophilin displays a functional and accessible reactive-site loop==
	<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>
Line 5:		Line 6:
	</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='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>
	<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='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='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'>[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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ody ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<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/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 31:		Line 32:
	==See Also==		==See Also==
	*[[Thrombin\|Thrombin]]		*[[Thrombin\|Thrombin]]
		+	*[[Thrombin heavy chain\|Thrombin heavy chain]]
		+	*[[Thrombin light chain\|Thrombin light chain]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:17, 12 September 2015

2015-09-12T02:17:12Z

←Older revision		Revision as of 02:17, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ody]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bos_taurus Bos taurus~~] and [http://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 [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 [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>
	</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='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>
	<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='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='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://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'>[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>
	</table>		</table>
	== Function ==		== 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/~~Q8WPI2_BOOMI Q8WPI2_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.	+	[[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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2ody" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Boophilus microplus]]
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
-	[[Category: Rhipicephalus microplus]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
	[[Category: Fuentes-Prior, P]]		[[Category: Fuentes-Prior, P]]

OCA at 22:34, 25 December 2014

2014-12-25T22:34:18Z

←Older revision		Revision as of 22:34, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ody]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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 [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 [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ODY FirstGlance]. <br>
-	</td></tr><tr><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><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>
-	<tr><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='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><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://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'>[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://www.rcsb.org/pdb/explore.do?structureId=2ody RCSB], [http://www.ebi.ac.uk/pdbsum/2ody PDBsum]</span></td></tr>
-	<table>	+	</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/Q8WPI2_BOOMI Q8WPI2_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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Rhipicephalus microplus]]		[[Category: Rhipicephalus microplus]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
-	[[Category: Fuentes-Prior, P.]]	+	[[Category: Fuentes-Prior, P]]
-	[[Category: Macedo-Ribeiro, S.]]	+	[[Category: Macedo-Ribeiro, S]]
-	[[Category: Pereira, P J.B.]]	+	[[Category: Pereira, P J.B]]
	[[Category: Blood clotting-blood clotting inhibitor complex]]		[[Category: Blood clotting-blood clotting inhibitor complex]]
	[[Category: Kunitz-type thrombin inhibitor]]		[[Category: Kunitz-type thrombin inhibitor]]

OCA at 09:52, 29 September 2014

2014-09-29T09:52:08Z

←Older revision		Revision as of 09:52, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2ody.~~png\|left~~\|200px]]	+	==Thrombin-bound boophilin displays a functional and accessible reactive-site loop==
		+	<StructureSection load='2ody' size='340' side='right' caption='[[2ody]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ody]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ODY FirstGlance]. <br>
		+	</td></tr><tr><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><br>
		+	<tr><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><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://www.rcsb.org/pdb/explore.do?structureId=2ody RCSB], [http://www.ebi.ac.uk/pdbsum/2ody PDBsum]</span></td></tr>
		+	<table>
		+	== 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>
		+	<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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inhibitors of coagulation factors from blood-feeding animals display a wide variety of structural motifs and inhibition mechanisms. We have isolated a novel inhibitor from the cattle tick Boophilus microplus, one of the most widespread parasites of farm animals. The inhibitor, which we have termed boophilin, has been cloned and overexpressed in Escherichia coli. Mature boophilin is composed of two canonical Kunitz-type domains, and inhibits not only the major procoagulant enzyme, thrombin, but in addition, and by contrast to all other previously characterised natural thrombin inhibitors, significantly interferes with the proteolytic activity of other serine proteinases such as trypsin and plasmin. The crystal structure of the bovine alpha-thrombin.boophilin complex, refined at 2.35 A resolution reveals a non-canonical binding mode to the proteinase. The N-terminal region of the mature inhibitor, Q16-R17-N18, binds in a parallel manner across the active site of the proteinase, with the guanidinium group of R17 anchored in the S(1) pocket, while the C-terminal Kunitz domain is negatively charged and docks into the basic exosite I of thrombin. This binding mode resembles the previously characterised thrombin inhibitor, ornithodorin which, unlike boophilin, is composed of two distorted Kunitz modules. Unexpectedly, both boophilin domains adopt markedly different orientations when compared to those of ornithodorin, in its complex with thrombin. The N-terminal boophilin domain rotates 9 degrees and is displaced by 6 A, while the C-terminal domain rotates almost 6 degrees accompanied by a 3 A displacement. The reactive-site loop of the N-terminal Kunitz domain of boophilin with its P(1) residue, K31, is fully solvent exposed and could thus bind a second trypsin-like proteinase without sterical restraints. This finding explains the formation of a ternary thrombin.boophilin.trypsin complex, and suggests a mechanism for prothrombinase inhibition in vivo.

-	~~{{STRUCTURE_2ody\| PDB=2ody \| SCENE= }}~~	+	Isolation, cloning and structural characterisation of boophilin, a multifunctional kunitz-type proteinase inhibitor from the cattle tick.,Macedo-Ribeiro S, Almeida C, Calisto BM, Friedrich T, Mentele R, Sturzebecher J, Fuentes-Prior P, Pereira PJ PLoS ONE. 2008 Feb 20;3(2):e1624. PMID:18286181<ref>PMID:18286181</ref>

-	~~===Thrombin-bound boophilin displays~~ a ~~functional and accessible reactive-site loop===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18286181}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2ody]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bos_taurus Bos taurus] and [http://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].~~	+

	==See Also==		==See Also==
	*[[Thrombin\|Thrombin]]		*[[Thrombin\|Thrombin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018286181<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Rhipicephalus microplus]]		[[Category: Rhipicephalus microplus]]

OCA at 22:26, 20 October 2012

2012-10-20T22:26:48Z

←Older revision		Revision as of 22:26, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2ody]] is a 6 chain structure ~~of [[Thrombin]]~~ with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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].	+	[[2ody]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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].

	==See Also==		==See Also==

OCA: Protected "2ody" [edit=sysop:move=sysop]

2012-07-27T16:19:24Z

Protected "2ody" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:19, 27 July 2012

OCA at 16:19, 27 July 2012

2012-07-27T16:19:23Z

←Older revision		Revision as of 16:19, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ody.png\|left\|200px]]		[[Image:2ody.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ody", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2ody\| PDB=2ody \| SCENE= }}		{{STRUCTURE_2ody\| PDB=2ody \| SCENE= }}

	===Thrombin-bound boophilin displays a functional and accessible reactive-site loop===		===Thrombin-bound boophilin displays a functional and accessible reactive-site loop===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18286181}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18286181 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18286181}}		{{ABSTRACT_PUBMED_18286181}}

	==About this Structure==		==About this Structure==
-	~~2ODY~~ is a 6 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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].	+	[[2ody]] is a 6 chain structure of [[Thrombin]] with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://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].
		+
		+	==See Also==
		+	*[[Thrombin\|Thrombin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18286181~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018286181</ref><references group="xtra"/>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Rhipicephalus microplus]]		[[Category: Rhipicephalus microplus]]
Line 30:		Line 21:
	[[Category: Macedo-Ribeiro, S.]]		[[Category: Macedo-Ribeiro, S.]]
	[[Category: Pereira, P J.B.]]		[[Category: Pereira, P J.B.]]
-	[[Category: Blood clotting/blood clotting inhibitor complex]]	+	[[Category: Blood clotting-blood clotting inhibitor complex]]
	[[Category: Kunitz-type thrombin inhibitor]]		[[Category: Kunitz-type thrombin inhibitor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:52:11 2009''