4ibl - Revision history

OCA at 15:19, 20 September 2023

2023-09-20T15:19:27Z

←Older revision		Revision as of 15:19, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ibl]] is a 3 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=4IBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ibl]] is a 3 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=4IBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IBL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [https://pdbe.org/4ibl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [https://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl 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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [https://pdbe.org/4ibl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [https://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:32, 15 March 2023

2023-03-15T10:32:11Z

←Older revision		Revision as of 10:32, 15 March 2023
Line 3:		Line 3:
	<StructureSection load='4ibl' size='340' side='right'caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4ibl' size='340' side='right'caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ibl]] is a 3 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=4IBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IBL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [https://pdbe.org/4ibl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [https://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl 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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [https://pdbe.org/4ibl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [https://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[https://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>	+	[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[https://omim.org/entry/227500 227500]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium. ~~[[https~~:~~//www.uniprot.org/uniprot/TF_HUMAN TF_HUMAN]] Initiates blood coagulation by forming a complex with circulating~~ factor ~~VII or~~ VIIa. ~~The [TF:VIIa] complex activates factors IX or~~ X ~~by specific limited protolysis~~. TF ~~plays a role~~ in ~~normal hemostasis~~ by ~~initiating~~ the ~~cell~~-~~surface assembly~~ and ~~propagation~~ of the ~~coagulation protease cascade~~.<ref>PMID:~~12652293~~</ref>	+	[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Coagulation factor VIIa (FVIIa) consists of a gamma-carboxyglutamic acid (GLA) domain, two epidermal growth factor-like (EGF) domains and a protease domain. FVIIa binds three Mg(2+) ions and four Ca(2+) ions in the GLA domain, one Ca(2+) ion in the EGF1 domain and one Ca(2+) ion in the protease domain. Further, FVIIa contains an Na(+) site in the protease domain. Since Na(+) and water share the same number of electrons, Na(+) sites in proteins are difficult to distinguish from waters in X-ray structures. Here, to verify the Na(+) site in FVIIa, the structure of the FVIIa-soluble tissue factor (TF) complex was solved at 1.8 A resolution containing Mg(2+), Ca(2+) and Rb(+) ions. In this structure, Rb(+) replaced two Ca(2+) sites in the GLA domain and occupied three non-metal sites in the protease domain. However, Rb(+) was not detected at the expected Na(+) site. In kinetic experiments, Na(+) increased the amidolytic activity of FVIIa towards the synthetic substrate S-2288 (H-D-Ile-Pro-Arg-p-nitroanilide) by approximately 20-fold; however, in the presence of Ca(2+), Na(+) had a negligible effect. Ca(2+) increased the hydrolytic activity of FVIIa towards S-2288 by approximately 60-fold in the absence of Na(+) and by approximately 82-fold in the presence of Na(+). In molecular-dynamics simulations, Na(+) stabilized the two Na(+)-binding loops (the 184-loop and 220-loop) and the TF-binding region spanning residues 163-180. Ca(2+) stabilized the Ca(2+)-binding loop (the 70-loop) and Na(+)-binding loops but not the TF-binding region. Na(+) and Ca(2+) together stabilized both the Na(+)-binding and Ca(2+)-binding loops and the TF-binding region. Previously, Rb(+) has been used to define the Na(+) site in thrombin; however, it was unsuccessful in detecting the Na(+) site in FVIIa. A conceivable explanation for this observation is provided.
		+
		+	Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium.,Vadivel K, Schmidt AE, Cascio D, Padmanabhan K, Krishnaswamy S, Brandstetter H, Bajaj SP Acta Crystallogr D Struct Biol. 2021 Jun 1;77(Pt 6):809-819. doi:, 10.1107/S2059798321003922. Epub 2021 May 14. PMID:34076594<ref>PMID:34076594</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ibl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[Factor VIIa 3D structures\|Factor VIIa 3D structures]]
	*[[Tissue factor\|Tissue factor]]		*[[Tissue factor\|Tissue factor]]
	== References ==		== References ==
Line 20:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Coagulation factor VIIa~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bajaj~~, S P~~]]	+	[[Category: Bajaj SP]]
-	[[Category: Cascio, D]]	+	[[Category: Cascio D]]
-	[[Category: Padmanabhan, K]]	+	[[Category: Padmanabhan K]]
-	[[Category: Schmidt, A]]	+	[[Category: Schmidt A]]
-	[[Category: Vadivel, K]]	+	[[Category: Vadivel K]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Serine protease]]~~	+
-	~~[[Category: Tissue factor~~]]	+

OCA at 12:15, 9 June 2021

2021-06-09T12:15:59Z

←Older revision		Revision as of 12:15, 9 June 2021
Line 3:		Line 3:
	<StructureSection load='4ibl' size='340' side='right'caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4ibl' size='340' side='right'caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IBL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [~~http~~://pdbe.org/4ibl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl 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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [https://pdbe.org/4ibl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [https://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[~~http~~://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>	+	[[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[https://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium. [[~~http~~://www.uniprot.org/uniprot/TF_HUMAN TF_HUMAN]] Initiates blood coagulation by forming a complex with circulating factor VII or VIIa. The [TF:VIIa] complex activates factors IX or X by specific limited protolysis. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade.<ref>PMID:12652293</ref>	+	[[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium. [[https://www.uniprot.org/uniprot/TF_HUMAN TF_HUMAN]] Initiates blood coagulation by forming a complex with circulating factor VII or VIIa. The [TF:VIIa] complex activates factors IX or X by specific limited protolysis. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade.<ref>PMID:12652293</ref>

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

OCA at 08:19, 27 March 2019

2019-03-27T08:19:26Z

←Older revision		Revision as of 08:19, 27 March 2019
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	==Rubidium Sites in Blood Coagulation Factor VIIa==		==Rubidium Sites in Blood Coagulation Factor VIIa==
-	<StructureSection load='4ibl' size='340' side='right' caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4ibl' size='340' side='right'caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IBL FirstGlance]. <br>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Coagulation factor VIIa]]		[[Category: Coagulation factor VIIa]]
		+	[[Category: Large Structures]]
	[[Category: Bajaj, S P]]		[[Category: Bajaj, S P]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]

OCA at 12:18, 11 August 2016

2016-08-11T12:18:12Z

←Older revision		Revision as of 12:18, 11 August 2016
Line 1:		Line 1:
		+
	==Rubidium Sites in Blood Coagulation Factor VIIa==		==Rubidium Sites in Blood Coagulation Factor VIIa==
	<StructureSection load='4ibl' size='340' side='right' caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4ibl' size='340' side='right' caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [http://www.ebi.ac.uk/pdbsum/4ibl 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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [http://pdbe.org/4ibl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [http://www.ebi.ac.uk/pdbsum/4ibl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ibl ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 14:27, 4 January 2015

2015-01-04T14:27:43Z

←Older revision		Revision as of 14:27, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4ibl~~\| ~~PDB~~=4ibl \| ~~SCENE~~= }}	+	==Rubidium Sites in Blood Coagulation Factor VIIa==
-	===~~Rubidium Sites in Blood~~ Coagulation ~~Factor~~ VIIa===	+	<StructureSection load='4ibl' size='340' side='right' caption='[[4ibl]], [[Resolution\|resolution]] 1.80Å' scene=''>
-		+	== Structural highlights ==
-	==Disease==	+	<table><tr><td colspan='2'>[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IBL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </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=4ibl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ibl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ibl RCSB], [http://www.ebi.ac.uk/pdbsum/4ibl PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[http://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>		[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[http://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>
-		+	== Function ==
-	==Function==	+
	[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium. [[http://www.uniprot.org/uniprot/TF_HUMAN TF_HUMAN]] Initiates blood coagulation by forming a complex with circulating factor VII or VIIa. The [TF:VIIa] complex activates factors IX or X by specific limited protolysis. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade.<ref>PMID:12652293</ref>		[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium. [[http://www.uniprot.org/uniprot/TF_HUMAN TF_HUMAN]] Initiates blood coagulation by forming a complex with circulating factor VII or VIIa. The [TF:VIIa] complex activates factors IX or X by specific limited protolysis. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade.<ref>PMID:12652293</ref>

-	==~~About this Structure~~==	+	==See Also==
-	[[~~4ibl~~]] ~~is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA].~~	+	*[[Tissue factor\|Tissue factor]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Coagulation factor VIIa]]		[[Category: Coagulation factor VIIa]]
-	[[Category: Bajaj, S P.]]	+	[[Category: Bajaj, S P]]
-	[[Category: Cascio, D.]]	+	[[Category: Cascio, D]]
-	[[Category: Padmanabhan, K.]]	+	[[Category: Padmanabhan, K]]
-	[[Category: Schmidt, A.]]	+	[[Category: Schmidt, A]]
-	[[Category: Vadivel, K.]]	+	[[Category: Vadivel, K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Serine protease]]		[[Category: Serine protease]]
	[[Category: Tissue factor]]		[[Category: Tissue factor]]

OCA at 10:00, 16 April 2014

2014-04-16T10:00:58Z

←Older revision		Revision as of 10:00, 16 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4ibl\| PDB=4ibl \| SCENE= }}
		+	===Rubidium Sites in Blood Coagulation Factor VIIa===

-	~~The~~ entry ~~4ibl is ON HOLD~~ ~~until Apr 16 2015~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[http://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>

-	~~Authors~~: ~~Vadivel, K~~.~~, Schmidt, A~~.~~, Cascio, D~~., ~~Padmanabhan~~, K., ~~Bajaj, S~~.P.	+	==Function==
		+	[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium. [[http://www.uniprot.org/uniprot/TF_HUMAN TF_HUMAN]] Initiates blood coagulation by forming a complex with circulating factor VII or VIIa. The [TF:VIIa] complex activates factors IX or X by specific limited protolysis. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade.<ref>PMID:12652293</ref>

-	~~Description~~: ~~Rubidium Sites in Blood~~ Coagulation ~~Factor~~ VIIa	+	==About this Structure==
		+	[[4ibl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IBL OCA].
		+
		+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Coagulation factor VIIa]]
		+	[[Category: Bajaj, S P.]]
		+	[[Category: Cascio, D.]]
		+	[[Category: Padmanabhan, K.]]
		+	[[Category: Schmidt, A.]]
		+	[[Category: Vadivel, K.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine protease]]
		+	[[Category: Tissue factor]]

OCA at 08:13, 2 April 2014

2014-04-02T08:13:52Z

←Older revision		Revision as of 08:13, 2 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ibl is ON HOLD until Apr 02 2015	+	The entry 4ibl is ON HOLD until Apr 16 2015

	Authors: Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.		Authors: Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.

	Description: Rubidium Sites in Blood Coagulation Factor VIIa		Description: Rubidium Sites in Blood Coagulation Factor VIIa

OCA at 08:29, 26 March 2014

2014-03-26T08:29:24Z

←Older revision		Revision as of 08:29, 26 March 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ibl is ON HOLD until ~~Paper Publication~~	+	The entry 4ibl is ON HOLD until Apr 02 2015

	Authors: Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.		Authors: Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.

	Description: Rubidium Sites in Blood Coagulation Factor VIIa		Description: Rubidium Sites in Blood Coagulation Factor VIIa

OCA at 08:54, 2 January 2013

2013-01-02T08:54:54Z

←Older revision		Revision as of 08:54, 2 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.		Authors: Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.

-	Description: ~~Sodium Site~~ in Blood Coagulation Factor VIIa	+	Description: Rubidium Sites in Blood Coagulation Factor VIIa