3s69 - Revision history

OCA at 10:39, 22 June 2022

OCA — Wed, 22 Jun 2022 10:39:56 GMT

←Older revision		Revision as of 10:39, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of saxthrombin==		==Crystal structure of saxthrombin==
-	<StructureSection load='3s69' size='340' side='right' caption='[[3s69]], [[Resolution\|resolution]] 1.43Å' scene=''>	+	<StructureSection load='3s69' size='340' side='right'caption='[[3s69]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S69 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S69 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [~~http~~://pdbe.org/3s69 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s69 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s69 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=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [https://pdbe.org/3s69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [https://www.ebi.ac.uk/pdbsum/3s69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s69 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VSPSX_GLOSA VSPSX_GLOSA]] Thrombin-like snake venom serine protease that shows strong blood coagulation activity in vitro.<ref>PMID:17671373</ref>	+	[[https://www.uniprot.org/uniprot/VSPSX_GLOSA VSPSX_GLOSA]] Thrombin-like snake venom serine protease that shows strong blood coagulation activity in vitro.<ref>PMID:17671373</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Gloydius saxatilis]]		[[Category: Gloydius saxatilis]]
		+	[[Category: Large Structures]]
	[[Category: Huang, K]]		[[Category: Huang, K]]
	[[Category: Niu, L]]		[[Category: Niu, L]]

OCA at 20:52, 4 August 2016

OCA — Thu, 04 Aug 2016 20:52:13 GMT

←Older revision		Revision as of 20:52, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of saxthrombin==		==Crystal structure of saxthrombin==
	<StructureSection load='3s69' size='340' side='right' caption='[[3s69]], [[Resolution\|resolution]] 1.43Å' scene=''>		<StructureSection load='3s69' size='340' side='right' caption='[[3s69]], [[Resolution\|resolution]] 1.43Å' scene=''>
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	<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S69 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S69 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [http://www.ebi.ac.uk/pdbsum/3s69 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=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [http://pdbe.org/3s69 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [http://www.ebi.ac.uk/pdbsum/3s69 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s69 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 3s69" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:04, 25 December 2014

OCA — Thu, 25 Dec 2014 13:04:14 GMT

←Older revision		Revision as of 13:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S69 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S69 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [http://www.ebi.ac.uk/pdbsum/3s69 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=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [http://www.ebi.ac.uk/pdbsum/3s69 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VSPSX_GLOSA VSPSX_GLOSA]] Thrombin-like snake venom serine protease that shows strong blood coagulation activity in vitro.<ref>PMID:17671373</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 12:		Line 14:
	Structure of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis.,Huang K, Zhao W, Gao Y, Wei W, Teng M, Niu L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):862-5. Epub, 2011 Jul 13. PMID:21821882<ref>PMID:21821882</ref>		Structure of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis.,Huang K, Zhao W, Gao Y, Wei W, Teng M, Niu L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):862-5. Epub, 2011 Jul 13. PMID:21821882<ref>PMID:21821882</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 19:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Gloydius saxatilis]]		[[Category: Gloydius saxatilis]]
-	[[Category: Huang, K.]]	+	[[Category: Huang, K]]
-	[[Category: Niu, L.]]	+	[[Category: Niu, L]]
-	[[Category: Teng, M.]]	+	[[Category: Teng, M]]
-	[[Category: Zhao, W.]]	+	[[Category: Zhao, W]]
	[[Category: Beta-barrel]]		[[Category: Beta-barrel]]
	[[Category: Fibrinogen binding]]		[[Category: Fibrinogen binding]]

OCA at 05:24, 5 June 2014

OCA — Thu, 05 Jun 2014 05:24:56 GMT

←Older revision		Revision as of 05:24, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3s69.~~jpg~~\|~~left\|200px~~]]	+	==Crystal structure of saxthrombin==
		+	<StructureSection load='3s69' size='340' side='right' caption='[[3s69]], [[Resolution\|resolution]] 1.43Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s69]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S69 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s69 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s69 RCSB], [http://www.ebi.ac.uk/pdbsum/3s69 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Snake-venom thrombin-like enzymes (SVTLEs) are serine proteases that are widely distributed in snakes from the Crotalinae subfamily of the Viperidae. In contrast to other snake-venom serine proteases, they have a biochemical activity similar to that of thrombin and play an important role in the process of blood coagulation. However, SVTLEs cannot activate factor VIII, which is essential in blood-clot stabilization. Consequently, blood clots produced by SVTLEs are not stable and are cleared rapidly. This characteristic makes SVTLEs attractive as potential candidates for antithrombotic therapy. Saxthrombin, an SVTLE from Gloydius saxatilis, was purified and crystallized to obtain a high-quality crystal, from which data were acquired to 1.43 A resolution. Preliminary X-ray diffraction analysis showed that the crystal belonged to space group C2, with unit-cell parameters a = 94.2, b = 52.2, c = 50.1 A, beta = 96.7 degrees . The crystal structure was determined by molecular replacement and the final R factor was 18.69%; the R(free) was 20.01%. This is the first report of a crystal structure of an SVTLE. Saxthrombin belongs to the typical alpha/beta-hydrolase fold of serine proteases. Its structure was compared with those of thrombin and other snake-venom serine proteases. The observed differences in the amino-acid composition of the loops surrounding the active site appear to contribute to different surface-charge distributions and thus alter the shape of the active-site cleft, which may explain the differences in substrate affinity.

-	<!--	+	Structure of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis.,Huang K, Zhao W, Gao Y, Wei W, Teng M, Niu L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):862-5. Epub, 2011 Jul 13. PMID:21821882<ref>PMID:21821882</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3s69"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded~~),	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3s69\| PDB=3s69 \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~saxthrombin===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21821882}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21821882 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21821882}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3s69]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021821882<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Gloydius saxatilis]]		[[Category: Gloydius saxatilis]]
	[[Category: Huang, K.]]		[[Category: Huang, K.]]

OCA at 06:00, 23 May 2012

OCA — Wed, 23 May 2012 06:00:34 GMT

←Older revision		Revision as of 06:00, 23 May 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3s69.jpg\|left\|200px]]

-	The ~~entry 3s69~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s69", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3s69\| PDB=3s69 \| SCENE= }}

-	~~Authors: Huang, K., Zhao, W., Teng, M., Niu, L.~~	+	===Crystal structure of saxthrombin===

-	~~Description~~: ~~Crystal~~ structure ~~of saxthrombin~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21821882}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21821882 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21821882}}
		+
		+	==About this Structure==
		+	[[3s69]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloydius_saxatilis Gloydius saxatilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S69 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021821882</ref><references group="xtra"/>
		+	[[Category: Gloydius saxatilis]]
		+	[[Category: Huang, K.]]
		+	[[Category: Niu, L.]]
		+	[[Category: Teng, M.]]
		+	[[Category: Zhao, W.]]
		+	[[Category: Beta-barrel]]
		+	[[Category: Fibrinogen binding]]
		+	[[Category: Glycosylation]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine enzyme]]

OCA at 08:34, 16 May 2012

OCA — Wed, 16 May 2012 08:34:09 GMT

←Older revision		Revision as of 08:34, 16 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s69 is ON HOLD until ~~sometime in the future~~	+	The entry 3s69 is ON HOLD until Paper Publication

-	Authors: Huang, K., Zhao, W., Teng, M.K., Niu, L.W.	+	Authors: Huang, K., Zhao, W., Teng, M., Niu, L.

	Description: Crystal structure of saxthrombin		Description: Crystal structure of saxthrombin

OCA at 06:03, 5 October 2011

OCA — Wed, 05 Oct 2011 06:03:58 GMT

←Older revision		Revision as of 06:03, 5 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s69 is ON HOLD	+	The entry 3s69 is ON HOLD until sometime in the future

	Authors: Huang, K., Zhao, W., Teng, M.K., Niu, L.W.		Authors: Huang, K., Zhao, W., Teng, M.K., Niu, L.W.

	Description: Crystal structure of saxthrombin		Description: Crystal structure of saxthrombin

OCA at 05:54, 15 June 2011

OCA — Wed, 15 Jun 2011 05:54:43 GMT

←Older revision		Revision as of 05:54, 15 June 2011
Line 3:		Line 3:
	The entry 3s69 is ON HOLD		The entry 3s69 is ON HOLD

-	Authors: Huang, K, Zhao, W, Teng, MK, Niu, LW	+	Authors: Huang, K., Zhao, W., Teng, M.K., Niu, L.W.

	Description: Crystal structure of saxthrombin		Description: Crystal structure of saxthrombin

OCA: Protected "3s69" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2011 05:27:48 GMT

Protected "3s69" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:27, 1 June 2011

OCA: New page: '''Unreleased structure''' The entry 3s69 is ON HOLD Authors: Huang, K, Zhao, W, Teng, MK, Niu, LW Description: Crystal structure of saxthrombin

OCA — Wed, 01 Jun 2011 05:27:47 GMT

New page: '''Unreleased structure''' The entry 3s69 is ON HOLD Authors: Huang, K, Zhao, W, Teng, MK, Niu, LW Description: Crystal structure of saxthrombin

New page

'''Unreleased structure'''

The entry 3s69 is ON HOLD

Authors: Huang, K, Zhao, W, Teng, MK, Niu, LW

Description: Crystal structure of saxthrombin