4i7y - Revision history

OCA at 08:47, 9 November 2022

2022-11-09T08:47:19Z

←Older revision		Revision as of 08:47, 9 November 2022
Line 3:		Line 3:
	<StructureSection load='4i7y' size='340' side='right'caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4i7y' size='340' side='right'caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i7y]] is a 3 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=4I7Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I7Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i7y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I7Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dih\|4dih]], [[4dii\|4dii]], [[3qlp\|3qlp]]</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=4i7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i7y OCA], [https://pdbe.org/4i7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i7y RCSB], [https://www.ebi.ac.uk/pdbsum/4i7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i7y ProSAT]</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=4i7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i7y OCA], [~~http~~://pdbe.org/4i7y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i7y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i7y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i7y 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 ==
Line 24:		Line 22:

	==See Also==		==See Also==
-	*[[Thrombin\|Thrombin]]	+	*[[Thrombin 3D Structures\|Thrombin 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 29:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thrombin]]~~	+	[[Category: Synthetic construct]]
-	~~[[Category: Krauss, I Russo~~]]	+	[[Category: Mazzarella L]]
-	[[Category: Mazzarella, L]]	+	[[Category: Merlino A]]
-	[[Category: Merlino, A]]	+	[[Category: Pica A]]
-	[[Category: Pica, A]]	+	[[Category: Russo Krauss I]]
-	[[Category: ~~Sica, F~~]]	+	[[Category: Sica F]]
-	[[Category: ~~Aptamer]]~~	+
-	~~[[Category: Blood]]~~	+
-	~~[[Category: Blood coagulation]]~~	+
-	~~[[Category: Dna aptamer]]~~	+
-	~~[[Category: Duplex-quadruplex junction]]~~	+
-	~~[[Category: G-quadruplex]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor-dna complex]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Serine protease]]~~	+
-	~~[[Category: Serine protease fold~~]]	+

OCA at 07:51, 27 March 2019

2019-03-27T07:51:47Z

←Older revision		Revision as of 07:51, 27 March 2019
Line 1:		Line 1:

	==Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II==		==Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II==
-	<StructureSection load='4i7y' size='340' side='right' caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4i7y' size='340' side='right'caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4i7y]] is a 3 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=4I7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I7Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4i7y]] is a 3 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=4I7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I7Y FirstGlance]. <br>
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
	[[Category: Krauss, I Russo]]		[[Category: Krauss, I Russo]]

OCA at 17:12, 11 August 2016

2016-08-11T17:12:52Z

←Older revision		Revision as of 17:12, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II==		==Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II==
	<StructureSection load='4i7y' size='340' side='right' caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4i7y' size='340' side='right' caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dih\|4dih]], [[4dii\|4dii]], [[3qlp\|3qlp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dih\|4dih]], [[4dii\|4dii]], [[3qlp\|3qlp]]</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=4i7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i7y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i7y RCSB], [http://www.ebi.ac.uk/pdbsum/4i7y 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=4i7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i7y OCA], [http://pdbe.org/4i7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i7y RCSB], [http://www.ebi.ac.uk/pdbsum/4i7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i7y ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	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 4i7y" style="background-color:#fffaf0;"></div>

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

OCA at 11:29, 20 January 2015

2015-01-20T11:29:54Z

←Older revision		Revision as of 11:29, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4i7y\| PDB=4i7y \| SCENE= }}~~	+	==Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II==
-	===Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II===	+	<StructureSection load='4i7y' size='340' side='right' caption='[[4i7y]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	{~~{ABSTRACT_PUBMED_24311581}~~}	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4i7y]] is a 3 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=4I7Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I7Y FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dih\|4dih]], [[4dii\|4dii]], [[3qlp\|3qlp]]</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=4i7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i7y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i7y RCSB], [http://www.ebi.ac.uk/pdbsum/4i7y 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 ==
		+	Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.

-	~~==Function==~~	+	Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer.,Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2403-11. doi:, 10.1107/S0907444913022269. Epub 2013 Nov 19. PMID:24311581<ref>PMID:24311581</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>
-	~~[[4i7y]] is~~ a ~~3 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=4I7Y OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024311581</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Thrombin\|Thrombin]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
-	[[Category: Krauss, I Russo.]]	+	[[Category: Krauss, I Russo]]
-	[[Category: Mazzarella, L.]]	+	[[Category: Mazzarella, L]]
-	[[Category: Merlino, A.]]	+	[[Category: Merlino, A]]
-	[[Category: Pica, A.]]	+	[[Category: Pica, A]]
-	[[Category: Sica, F.]]	+	[[Category: Sica, F]]
	[[Category: Aptamer]]		[[Category: Aptamer]]
	[[Category: Blood]]		[[Category: Blood]]

OCA at 10:44, 1 January 2014

2014-01-01T10:44:42Z

←Older revision		Revision as of 10:44, 1 January 2014
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	{{STRUCTURE_4i7y\| PDB=4i7y \| SCENE= }}		{{STRUCTURE_4i7y\| PDB=4i7y \| SCENE= }}
	===Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II===		===Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II===
-	{{~~ABSTRACT_PUBMED_22669903~~}}	+	{{ABSTRACT_PUBMED_24311581}}

	==Disease==		==Disease==
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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~022669903~~</ref><references group="xtra"/><references/>	+	<ref group="xtra">PMID:024311581</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thrombin]]		[[Category: Thrombin]]

OCA at 12:15, 11 December 2013

2013-12-11T12:15:02Z

←Older revision		Revision as of 12:15, 11 December 2013
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	{{STRUCTURE_4i7y\| PDB=4i7y \| SCENE= }}		{{STRUCTURE_4i7y\| PDB=4i7y \| SCENE= }}
	===Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II===		===Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II===
-	{{~~ABSTRACT_PUBMED_21715374~~}}	+	{{ABSTRACT_PUBMED_22669903}}

	==Disease==		==Disease==
Line 13:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~021715374~~</ref><references group="xtra"/><references/>	+	<ref group="xtra">PMID:022669903</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Thrombin]]		[[Category: Thrombin]]

OCA at 07:58, 16 October 2013

2013-10-16T07:58:46Z

←Older revision		Revision as of 07:58, 16 October 2013
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4i7y\| PDB=4i7y \| SCENE= }}
		+	===Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II===
		+	{{ABSTRACT_PUBMED_21715374}}

-	The entry ~~4i7y~~ 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~~: ~~Pica, A~~., ~~Russo Krauss~~, I., ~~Merlino~~, A., ~~Mazzarella~~, L., ~~Sica~~, F.	+	==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: Crystal~~ Structure ~~of Human Alpha Thrombin in Complex with~~ a 27-~~mer~~ Aptamer ~~Bound to Exosite II~~	+	==About this Structure==
		+	[[4i7y]] is a 3 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=4I7Y OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021715374</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Thrombin]]
		+	[[Category: Krauss, I Russo.]]
		+	[[Category: Mazzarella, L.]]
		+	[[Category: Merlino, A.]]
		+	[[Category: Pica, A.]]
		+	[[Category: Sica, F.]]
		+	[[Category: Aptamer]]
		+	[[Category: Blood]]
		+	[[Category: Blood coagulation]]
		+	[[Category: Dna aptamer]]
		+	[[Category: Duplex-quadruplex junction]]
		+	[[Category: G-quadruplex]]
		+	[[Category: Hydrolase-hydrolase inhibitor-dna complex]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Serine protease]]
		+	[[Category: Serine protease fold]]

OCA at 08:53, 2 January 2013

2013-01-02T08:53:49Z

←Older revision		Revision as of 08:53, 2 January 2013
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i7y is ON HOLD	+	The entry 4i7y is ON HOLD until Paper Publication

	Authors: Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.		Authors: Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

	Description: Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II		Description: Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II

OCA: Protected "4i7y" [edit=sysop:move=sysop]

2012-12-12T20:50:00Z

Protected "4i7y" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:50, 12 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i7y is ON HOLD Authors: Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F. Description: Crystal Structure of Human Alpha Thrombin i...

2012-12-12T20:49:59Z

New page: '''Unreleased structure''' The entry 4i7y is ON HOLD Authors: Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F. Description: Crystal Structure of Human Alpha Thrombin i...

New page

'''Unreleased structure'''

The entry 4i7y is ON HOLD

Authors: Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

Description: Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II