4y3k - Revision history

OCA at 10:52, 10 January 2024

OCA — Wed, 10 Jan 2024 10:52:23 GMT

←Older revision		Revision as of 10:52, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y3k]] is a 2 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=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y3k]] is a 2 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=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [https://pdbe.org/4y3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [https://www.ebi.ac.uk/pdbsum/4y3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3k 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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [https://pdbe.org/4y3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [https://www.ebi.ac.uk/pdbsum/4y3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3k ProSAT]</span></td></tr>
	</table>		</table>

OCA at 18:05, 26 April 2023

OCA — Wed, 26 Apr 2023 18:05:07 GMT

←Older revision		Revision as of 18:05, 26 April 2023
Line 1:		Line 1:

	==Structure of Vaspin mutant E379S==		==Structure of Vaspin mutant E379S==
-	<StructureSection load='4y3k' size='340' side='right' caption='[[4y3k]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4y3k' size='340' side='right'caption='[[4y3k]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y3k]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y3k]] is a 2 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=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4if8\|4if8]], [[4y40\|4y40]]</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [https://pdbe.org/4y3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [https://www.ebi.ac.uk/pdbsum/4y3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3k ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SERPINA12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [~~http~~://pdbe.org/4y3k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y3k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3k ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SPA12_HUMAN SPA12_HUMAN]] May modulate insulin action conceivably only in the presence of its yet undefined target proteases in white adipose tissues.	+	[https://www.uniprot.org/uniprot/SPA12_HUMAN SPA12_HUMAN] May modulate insulin action conceivably only in the presence of its yet undefined target proteases in white adipose tissues.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4y3k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4y3k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serpin 3D structures\|Serpin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Heiker~~, J T~~]]	+	[[Category: Large Structures]]
-	[[Category: Meier, R]]	+	[[Category: Heiker JT]]
-	[[Category: Pippel, J]]	+	[[Category: Meier R]]
-	[[Category: Schultz, S]]	+	[[Category: Pippel J]]
-	[[Category: Strater, N]]	+	[[Category: Schultz S]]
-	[[Category: Ulbricht, D]]	+	[[Category: Strater N]]
-	~~[[Category: Adipokine]]~~	+	[[Category: Ulbricht D]]
-	~~[[Category: Exosite]]~~	+
-	~~[[Category: Hydrolase inhibitor]]~~	+
-	~~[[Category: Serpin~~]]	+

OCA at 17:51, 16 November 2017

OCA — Thu, 16 Nov 2017 17:51:13 GMT

←Older revision		Revision as of 17:51, 16 November 2017
Line 1:		Line 1:
		+
	==Structure of Vaspin mutant E379S==		==Structure of Vaspin mutant E379S==
	<StructureSection load='4y3k' size='340' side='right' caption='[[4y3k]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4y3k' size='340' side='right' caption='[[4y3k]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y3k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y3k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4if8\|4if8]], [[4y40\|4y40]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4if8\|4if8]], [[4y40\|4y40]]</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [http://pdbe.org/4y3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [http://www.ebi.ac.uk/pdbsum/4y3k PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SERPINA12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [http://pdbe.org/4y3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [http://www.ebi.ac.uk/pdbsum/4y3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Heiker, J T]]		[[Category: Heiker, J T]]
	[[Category: Meier, R]]		[[Category: Meier, R]]

OCA at 07:13, 30 September 2015

OCA — Wed, 30 Sep 2015 07:13:58 GMT

←Older revision		Revision as of 07:13, 30 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4if8\|4if8]], [[4y40\|4y40]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4if8\|4if8]], [[4y40\|4y40]]</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [http://www.ebi.ac.uk/pdbsum/4y3k 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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [http://pdbe.org/4y3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [http://www.ebi.ac.uk/pdbsum/4y3k PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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 4y3k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:31, 12 August 2015

OCA — Wed, 12 Aug 2015 14:31:36 GMT

←Older revision		Revision as of 14:31, 12 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of Vaspin mutant E379S==
		+	<StructureSection load='4y3k' size='340' side='right' caption='[[4y3k]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4y3k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y3K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4if8\|4if8]], [[4y40\|4y40]]</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=4y3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y3k RCSB], [http://www.ebi.ac.uk/pdbsum/4y3k PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SPA12_HUMAN SPA12_HUMAN]] May modulate insulin action conceivably only in the presence of its yet undefined target proteases in white adipose tissues.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SerpinA12 (vaspin) is thought to be mainly expressed in adipose tissue and has multiple beneficial effects on metabolic, inflammatory and atherogenic processes related to obesity. Kallikrein 7 (KLK7) is the only known protease target of vaspin to date and is inhibited with a moderate inhibition rate. In the crystal structure, the cleavage site (P1-P1') of the vaspin reactive center loop is fairly rigid compared to the flexible residues before P2, possibly supported by an ionic interaction of P1' glutamate (Glu379) with an arginine residue (Arg302) of the beta-sheet C. A P1' glutamate seems highly unusual and unfavorable for the protease KLK7. We characterized vaspin mutants to investigate the roles of these two residues in protease inhibition and recognition by vaspin. RCL mutations changing the P1' residue or altering RCL conformation significantly increased inhibition parameters while removal of the positive charge within beta-sheet C impeded the serpin-protease interaction. Arg302 is a crucial contact to enable vaspin recognition by KLK7 and it supports moderate inhibition of the serpin despite the presence of the detrimental P1' Glu379, which clearly represents a major limiting factor for vaspin inhibitory activity. We also show that the vaspin inhibition rate for KLK7 can be modestly increased by heparin and demonstrate that vaspin is a heparin-binding serpin. Noteworthy, we observed vaspin as a remarkably thermostable serpin and found residues Glu379 and Arg302 influencing heat-induced polymerization. These structural and functional results reveal the mechanistic basis of how reactive center loop sequence and exosite interaction in vaspin enable KLK7 recognition and regulate protease inhibition as well as stability of this adipose tissue derived serpin.

-	~~The entry 4y3k is ON HOLD until Paper Publication~~	+	A unique serpin P1' glutamate and a conserved beta-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin).,Ulbricht D, Pippel J, Schultz S, Meier R, Strater N, Heiker JT Biochem J. 2015 Jul 21. pii: BJ20150643. PMID:26199422<ref>PMID:26199422</ref>

-	~~Authors: Pippel~~, J.~~, Strater, N., Ulbricht, D., Schultz,~~ S.~~, Meier, R., Heiker, J.T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description:~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	[[Category: Heiker, J.T]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Heiker, J T]]
	[[Category: Meier, R]]		[[Category: Meier, R]]
		+	[[Category: Pippel, J]]
	[[Category: Schultz, S]]		[[Category: Schultz, S]]
		+	[[Category: Strater, N]]
	[[Category: Ulbricht, D]]		[[Category: Ulbricht, D]]
-	[[Category: ~~Pippel, J~~]]	+	[[Category: Adipokine]]
-	[[Category: ~~Strater, N~~]]	+	[[Category: Exosite]]
		+	[[Category: Hydrolase inhibitor]]
		+	[[Category: Serpin]]

OCA at 12:38, 25 February 2015

OCA — Wed, 25 Feb 2015 12:38:38 GMT

←Older revision		Revision as of 12:38, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y3k is ON HOLD	+	The entry 4y3k is ON HOLD until Paper Publication

	Authors: Pippel, J., Strater, N., Ulbricht, D., Schultz, S., Meier, R., Heiker, J.T.		Authors: Pippel, J., Strater, N., Ulbricht, D., Schultz, S., Meier, R., Heiker, J.T.

OCA: Protected "4y3k" [edit=sysop:move=sysop]

OCA — Wed, 18 Feb 2015 11:59:31 GMT

Protected "4y3k" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:59, 18 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y3k is ON HOLD Authors: Pippel, J., Strater, N., Ulbricht, D., Schultz, S., Meier, R., Heiker, J.T. Description: [[Category: Unreleased Structure...

OCA — Wed, 18 Feb 2015 11:59:29 GMT

New page: '''Unreleased structure''' The entry 4y3k is ON HOLD Authors: Pippel, J., Strater, N., Ulbricht, D., Schultz, S., Meier, R., Heiker, J.T. Description: [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 4y3k is ON HOLD

Authors: Pippel, J., Strater, N., Ulbricht, D., Schultz, S., Meier, R., Heiker, J.T.

Description:
[[Category: Unreleased Structures]]
[[Category: Heiker, J.T]]
[[Category: Meier, R]]
[[Category: Schultz, S]]
[[Category: Ulbricht, D]]
[[Category: Pippel, J]]
[[Category: Strater, N]]