6t54 - Revision history

OCA at 11:51, 1 February 2024

OCA — Thu, 01 Feb 2024 11:51:58 GMT

←Older revision		Revision as of 11:51, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6t54]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T54 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6t54]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T54 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MJK:(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide'>MJK</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</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]] 1.57Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MJK:(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide'>MJK</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</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=6t54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t54 OCA], [https://pdbe.org/6t54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t54 RCSB], [https://www.ebi.ac.uk/pdbsum/6t54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t54 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=6t54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t54 OCA], [https://pdbe.org/6t54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t54 RCSB], [https://www.ebi.ac.uk/pdbsum/6t54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t54 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:27, 7 December 2022

OCA — Wed, 07 Dec 2022 08:27:24 GMT

←Older revision		Revision as of 08:27, 7 December 2022
Line 1:		Line 1:

-	====	+	==Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative==
-	<StructureSection load='6t54' size='340' side='right'caption='[[6t54]]' scene=''>	+	<StructureSection load='6t54' size='340' side='right'caption='[[6t54]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t54]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T54 FirstGlance]. <br>
-	</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=6t54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t54 OCA], [~~http~~://pdbe.org/6t54 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6t54 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6t54 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6t54 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MJK:(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide'>MJK</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</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=6t54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t54 OCA], [https://pdbe.org/6t54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t54 RCSB], [https://www.ebi.ac.uk/pdbsum/6t54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t54 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[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 ==
		+	[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>
		+
		+	==See Also==
		+	*[[Hirudin 3D structures\|Hirudin 3D structures]]
		+	*[[Thrombin 3D Structures\|Thrombin 3D Structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hirudo medicinalis]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Abazi N]]
		+	[[Category: Heine A]]
		+	[[Category: Klebe G]]
		+	[[Category: Ngo K]]

OCA at 09:33, 18 November 2020

OCA — Wed, 18 Nov 2020 09:33:35 GMT

←Older revision		Revision as of 09:33, 18 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6t54 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6t54' size='340' side='right'caption='[[6t54]]' scene=''>
-	~~Authors~~: ~~Ngo, K~~.~~, Abazi, N~~.~~, Heine, A~~.~~, Klebe, G~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Thrombin in Complex with~~ a ~~D-Phe-Pro-2-bromothiophene Derivative~~	+	</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=6t54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t54 OCA], [http://pdbe.org/6t54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t54 RCSB], [http://www.ebi.ac.uk/pdbsum/6t54 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t54 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	</table>
-	[[~~Category~~: ~~Ngo~~, K]]	+	__TOC__
-	[~~[Category~~: ~~Abazi~~, N]]	+	</StructureSection>
-	[[Category: ~~Heine, A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Klebe, G~~]]	+	[[Category: Z-disk]]

OCA: Protected "6t54" [edit=sysop:move=sysop]

OCA — Wed, 23 Oct 2019 05:02:31 GMT

Protected "6t54" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:02, 23 October 2019

OCA: New page: '''Unreleased structure''' The entry 6t54 is ON HOLD until Paper Publication Authors: Ngo, K., Abazi, N., Heine, A., Klebe, G. Description: Thrombin in Complex with a D-Phe-Pro-2-bromo...

OCA — Wed, 23 Oct 2019 05:02:29 GMT

New page: '''Unreleased structure''' The entry 6t54 is ON HOLD until Paper Publication Authors: Ngo, K., Abazi, N., Heine, A., Klebe, G. Description: Thrombin in Complex with a D-Phe-Pro-2-bromo...

New page

'''Unreleased structure'''

The entry 6t54 is ON HOLD until Paper Publication

Authors: Ngo, K., Abazi, N., Heine, A., Klebe, G.

Description: Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative
[[Category: Unreleased Structures]]
[[Category: Ngo, K]]
[[Category: Abazi, N]]
[[Category: Heine, A]]
[[Category: Klebe, G]]