3vxf - Revision history

OCA at 19:08, 27 July 2022

OCA — Wed, 27 Jul 2022 19:08:48 GMT

OCA at 10:47, 9 September 2020

OCA — Wed, 09 Sep 2020 10:47:16 GMT

←Older revision		Revision as of 10:47, 9 September 2020
Line 1:		Line 1:

	==X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5==		==X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5==
-	<StructureSection load='3vxf' size='340' side='right' caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3vxf' size='340' side='right'caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VXF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3VXF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxe\|3vxe]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxe\|3vxe]]</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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [http://pdbe.org/3vxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [http://www.ebi.ac.uk/pdbsum/3vxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vxf 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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [http://pdbe.org/3vxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [http://www.ebi.ac.uk/pdbsum/3vxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vxf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 25:		Line 25:

	==See Also==		==See Also==
-	*[[Thrombin\|Thrombin]]	+	*[[Thrombin 3D Structures\|Thrombin 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
	[[Category: Kurihara, K]]		[[Category: Kurihara, K]]

OCA at 20:40, 2 December 2018

OCA — Sun, 02 Dec 2018 20:40:12 GMT

←Older revision		Revision as of 20:40, 2 December 2018
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	</div>		</div>
	<div class="pdbe-citations 3vxf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3vxf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thrombin\|Thrombin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:59, 22 November 2017

OCA — Wed, 22 Nov 2017 07:59:02 GMT

←Older revision		Revision as of 07:59, 22 November 2017
Line 23:		Line 23:
	</div>		</div>
	<div class="pdbe-citations 3vxf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3vxf" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thrombin\|Thrombin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:46, 4 August 2016

OCA — Thu, 04 Aug 2016 10:46:40 GMT

←Older revision		Revision as of 10:46, 4 August 2016
Line 1:		Line 1:
		+
	==X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5==		==X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5==
	<StructureSection load='3vxf' size='340' side='right' caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3vxf' size='340' side='right' caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxe\|3vxe]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxe\|3vxe]]</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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [http://www.ebi.ac.uk/pdbsum/3vxf 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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [http://pdbe.org/3vxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [http://www.ebi.ac.uk/pdbsum/3vxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vxf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	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 3vxf" style="background-color:#fffaf0;"></div>

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

OCA at 07:32, 21 December 2014

OCA — Sun, 21 Dec 2014 07:32:50 GMT

←Older revision		Revision as of 07:32, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3vxf\| PDB=3vxf \| SCENE= }}~~	+	==X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5==
-	===X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5===	+	<StructureSection load='3vxf' size='340' side='right' caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23712263}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3vxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VXF FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxe\|3vxe]]</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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [http://www.ebi.ac.uk/pdbsum/3vxf PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[http://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[http://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[http://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[http://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>		[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[http://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[http://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[http://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[http://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] 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.<ref>PMID:2856554</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The protonation states and hydration structures of the alpha-thrombin-bivalirudin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8A, respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25A resolution. The complex represents a model of the enzyme-product (EP) complex of alpha-thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for Ddelta1 and Depsilon2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen Ogamma of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the Ogamma atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.

-	~~==Function==~~	+	Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex.,Yamada T, Kurihara K, Ohnishi Y, Tamada T, Tomoyori K, Masumi K, Tanaka I, Kuroki R, Niimura N Biochim Biophys Acta. 2013 Aug;1834(8):1532-8. doi: 10.1016/j.bbapap.2013.05.014., Epub 2013 May 25. PMID:23712263<ref>PMID:23712263</ref>
-	~~[[http~~:~~//www~~.~~uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] 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~~.<ref>PMID:~~2856554~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3vxf]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:023712263</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Thrombin\|Thrombin]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
-	[[Category: Kurihara, K.]]	+	[[Category: Kurihara, K]]
-	[[Category: Kuroki, R.]]	+	[[Category: Kuroki, R]]
-	[[Category: Masumi, K.]]	+	[[Category: Masumi, K]]
-	[[Category: Niimura, N.]]	+	[[Category: Niimura, N]]
-	[[Category: Ohnishi, Y.]]	+	[[Category: Ohnishi, Y]]
-	[[Category: Tamada, T.]]	+	[[Category: Tamada, T]]
-	[[Category: Tanaka, I.]]	+	[[Category: Tanaka, I]]
-	[[Category: Tomoyori, K.]]	+	[[Category: Tomoyori, K]]
-	[[Category: Yamada, T.]]	+	[[Category: Yamada, T]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Hydrolysis]]		[[Category: Hydrolysis]]
	[[Category: Serine protease]]		[[Category: Serine protease]]

OCA at 10:47, 4 September 2013

OCA — Wed, 04 Sep 2013 10:47:00 GMT

←Older revision		Revision as of 10:47, 4 September 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3vxf\| PDB=3vxf \| SCENE= }}
		+	===X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5===
		+	{{ABSTRACT_PUBMED_23712263}}

-	The entry ~~3vxf~~ is ~~ON HOLD~~ until ~~Paper Publication~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[http://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[http://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[http://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[http://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>

-	~~Authors~~: ~~Yamada, T~~.~~, Kurihara, K~~., ~~Masumi~~, K., ~~Tamada~~, T., ~~Tomoyori~~, K., ~~Ohnishi~~, Y., ~~Tanaka, I., Kuroki, R, Niimura, N~~.	+	==Function==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] 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.<ref>PMID:2856554</ref>

-	~~Description~~: X/N ~~Joint refinement of Human alpha~~-~~thrombin-Bivalirudin~~ complex ~~PD5~~	+	==About this Structure==
		+	[[3vxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023712263</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Thrombin]]
		+	[[Category: Kurihara, K.]]
		+	[[Category: Kuroki, R.]]
		+	[[Category: Masumi, K.]]
		+	[[Category: Niimura, N.]]
		+	[[Category: Ohnishi, Y.]]
		+	[[Category: Tamada, T.]]
		+	[[Category: Tanaka, I.]]
		+	[[Category: Tomoyori, K.]]
		+	[[Category: Yamada, T.]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Hydrolysis]]
		+	[[Category: Serine protease]]

OCA at 06:55, 24 October 2012

OCA — Wed, 24 Oct 2012 06:55:07 GMT

←Older revision		Revision as of 06:55, 24 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vxf is ON HOLD	+	The entry 3vxf is ON HOLD until Paper Publication

	Authors: Yamada, T., Kurihara, K., Masumi, K., Tamada, T., Tomoyori, K., Ohnishi, Y., Tanaka, I., Kuroki, R, Niimura, N.		Authors: Yamada, T., Kurihara, K., Masumi, K., Tamada, T., Tomoyori, K., Ohnishi, Y., Tanaka, I., Kuroki, R, Niimura, N.

	Description: X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5		Description: X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

OCA at 06:40, 10 October 2012

OCA — Wed, 10 Oct 2012 06:40:25 GMT

←Older revision		Revision as of 06:40, 10 October 2012
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	Authors: Yamada, T., Kurihara, K., Masumi, K., Tamada, T., Tomoyori, K., Ohnishi, Y., Tanaka, I., Kuroki, R, Niimura, N.		Authors: Yamada, T., Kurihara, K., Masumi, K., Tamada, T., Tomoyori, K., Ohnishi, Y., Tanaka, I., Kuroki, R, Niimura, N.

-	Description: X/N ~~JOINT REFINEMENT OF HUMAN ALPHA~~-~~THROMBIN~~ -~~BIVALIRUDIN COMPLEX~~ PD5	+	Description: X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

OCA: Protected "3vxf" [edit=sysop:move=sysop]

OCA — Wed, 19 Sep 2012 06:41:34 GMT

Protected "3vxf" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:41, 19 September 2012

←Older revision		Revision as of 19:08, 27 July 2022
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	<StructureSection load='3vxf' size='340' side='right'caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3vxf' size='340' side='right'caption='[[3vxf]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vxf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3VXF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vxf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VXF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxe\|3vxe]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vxe\|3vxe]]</div></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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [~~http~~://pdbe.org/3vxf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vxf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vxf 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=3vxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vxf OCA], [https://pdbe.org/3vxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vxf RCSB], [https://www.ebi.ac.uk/pdbsum/3vxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vxf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[~~http~~://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[~~http~~://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[~~http~~://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[~~http~~://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>	+	[[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[https://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[https://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[https://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[https://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] 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.<ref>PMID:2856554</ref>	+	[[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] 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.<ref>PMID:2856554</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==