5jw1 - Revision history

OCA at 19:12, 20 September 2023

OCA — Wed, 20 Sep 2023 19:12:12 GMT

←Older revision		Revision as of 19:12, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jw1' size='340' side='right'caption='[[5jw1]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='5jw1' size='340' side='right'caption='[[5jw1]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jw1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JW1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jw1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CEL:4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE'>CEL</scene>, <scene name='pdbligand=COH:PROTOPORPHYRIN+IX+CONTAINING+CO'>COH</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.822Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jvy\|5jvy]], [[5jvz\|5jvz]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CEL:4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE'>CEL</scene>, <scene name='pdbligand=COH:PROTOPORPHYRIN+IX+CONTAINING+CO'>COH</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5jw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jw1 OCA], [https://pdbe.org/5jw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jw1 RCSB], [https://www.ebi.ac.uk/pdbsum/5jw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jw1 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/Prostaglandin-endoperoxide_synthase Prostaglandin-endoperoxide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.1 1.14.99.1] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jw1 OCA], [~~http~~://pdbe.org/5jw1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jw1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jw1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jw1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PGH2_MOUSE PGH2_MOUSE]] Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.<ref>PMID:12925531</ref> <ref>PMID:20463020</ref> <ref>PMID:20810665</ref> <ref>PMID:21489986</ref>	+	[https://www.uniprot.org/uniprot/PGH2_MOUSE PGH2_MOUSE] Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.<ref>PMID:12925531</ref> <ref>PMID:20463020</ref> <ref>PMID:20810665</ref> <ref>PMID:21489986</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: Prostaglandin-endoperoxide synthase~~]]	+	[[Category: Malkowski MG]]
-	[[Category: Malkowski~~, M G~~]]	+	[[Category: Orlando BJ]]
-	[[Category: Orlando~~, B J]]~~	+
-	~~[[Category: Celebrex]]~~	+
-	~~[[Category: Celecoxib]]~~	+
-	~~[[Category: Cox-2]]~~	+
-	~~[[Category: Coxib]]~~	+
-	~~[[Category: Cyclooxygenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:42, 17 June 2020

OCA — Wed, 17 Jun 2020 11:42:26 GMT

←Older revision		Revision as of 11:42, 17 June 2020
Line 1:		Line 1:

	==Crystal structure of Celecoxib bound to S121P murine COX-2 mutant==		==Crystal structure of Celecoxib bound to S121P murine COX-2 mutant==
-	<StructureSection load='5jw1' size='340' side='right' caption='[[5jw1]], [[Resolution\|resolution]] 2.82Å' scene=''>	+	<StructureSection load='5jw1' size='340' side='right'caption='[[5jw1]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jw1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JW1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jw1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JW1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CEL:4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE'>CEL</scene>, <scene name='pdbligand=COH:PROTOPORPHYRIN+IX+CONTAINING+CO'>COH</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=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CEL:4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE'>CEL</scene>, <scene name='pdbligand=COH:PROTOPORPHYRIN+IX+CONTAINING+CO'>COH</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">[[5jvy\|5jvy]], [[5jvz\|5jvz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jvy\|5jvy]], [[5jvz\|5jvz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-endoperoxide_synthase Prostaglandin-endoperoxide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.1 1.14.99.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-endoperoxide_synthase Prostaglandin-endoperoxide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.1 1.14.99.1] </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=5jw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jw1 OCA], [http://pdbe.org/5jw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jw1 RCSB], [http://www.ebi.ac.uk/pdbsum/5jw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jw1 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jw1 OCA], [http://pdbe.org/5jw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jw1 RCSB], [http://www.ebi.ac.uk/pdbsum/5jw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jw1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PGH2_MOUSE PGH2_MOUSE]] Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.<ref>PMID:12925531</ref> <ref>PMID:20463020</ref> <ref>PMID:20810665</ref> <ref>PMID:21489986</ref>		[[http://www.uniprot.org/uniprot/PGH2_MOUSE PGH2_MOUSE]] Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.<ref>PMID:12925531</ref> <ref>PMID:20463020</ref> <ref>PMID:20810665</ref> <ref>PMID:21489986</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Prostaglandin endoperoxide H synthase-2 (PGHS-2), also called cyclooxygenase-2 (COX-2), converts arachidonic acid to PGH2 PGHS-2 is a conformational heterodimer composed of allosteric (Eallo) and catalytic (Ecat) subunits. Fatty acids (FAs) bind to Arg-120 of Eallo increasing to different degrees, depending on the FA, the Vmax of its Ecat partner. We report here that movement of helical residues 120-122 and loop residues 123-129 of Eallo underlies the allosteric effects of FAs and allosteric COX-2 inhibitors, including naproxen and flurbiprofen. An S121P substitution in both PGHS-2 monomers yields a variant (S121P/S121P PGHS-2) that has 1.7-1.8 times the Vmax of native PGHS-2 and is relatively insensitive to activation by FAs or inhibition by allosteric inhibitors. The S121P substitution in Eallo is primarily responsible for these effects. In X-ray crystal structures, the Calpha atoms of helical residues 119-122 of S121P/S121P PGHS-2 are displaced from their normal positions. Additionally, the S121P/S121P PGHS-2 variants in which Pro-127 and Ser-541 are replaced by cysteines spontaneously forms Cys-127 to Cys-541 cross-links between monomers. This is unlike the corresponding native PGHS-2 variant and suggests that S121P substitutions also unhinge the loop involving residues 123-129. We conclude the following: (a) the region involving residues 120-129 of unoccupied Eallo tonically inhibits Ecat; (b) binding of an activating FA (e.g. arachidonic, palmitic, or oleic acid) to Eallo or an S121P substitution in Eallo repositions this region to increase Ecat activity; and (c) allosteric COX inhibitors act by preventing FA binding to Eallo and additionally by relocating Eallo residues to inhibit Ecat.
		+
		+	Fatty Acid Binding to the Allosteric Subunit of Cyclooxygenase-2 Relieves a Tonic Inhibition of the Catalytic Subunit.,Dong L, Yuan C, Orlando BJ, Malkowski MG, Smith WL J Biol Chem. 2016 Dec 2;291(49):25641-25655. doi: 10.1074/jbc.M116.757310. Epub, 2016 Oct 18. PMID:27756840<ref>PMID:27756840</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jw1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cyclooxygenase 3D structures\|Cyclooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Prostaglandin-endoperoxide synthase]]		[[Category: Prostaglandin-endoperoxide synthase]]
	[[Category: Malkowski, M G]]		[[Category: Malkowski, M G]]

OCA at 18:46, 26 October 2016

OCA — Wed, 26 Oct 2016 18:46:49 GMT

←Older revision		Revision as of 18:46, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jw1 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Celecoxib bound to S121P murine COX-2 mutant==
-		+	<StructureSection load='5jw1' size='340' side='right' caption='[[5jw1]], [[Resolution\|resolution]] 2.82Å' scene=''>
-	~~Authors~~: ~~Malkowski~~, M.G., ~~Orlando~~, B.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jw1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JW1 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~Celecoxib bound to S121P murine COX~~-~~2 mutant~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CEL:4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE'>CEL</scene>, <scene name='pdbligand=COH:PROTOPORPHYRIN+IX+CONTAINING+CO'>COH</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jvy\|5jvy]], [[5jvz\|5jvz]]</td></tr>
-	[[Category: Orlando, B.J]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prostaglandin-endoperoxide_synthase Prostaglandin-endoperoxide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.1 1.14.99.1] </span></td></tr>
-	[[Category: ~~Malkowski, M.G~~]]	+	<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=5jw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jw1 OCA], [http://pdbe.org/5jw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jw1 RCSB], [http://www.ebi.ac.uk/pdbsum/5jw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jw1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PGH2_MOUSE PGH2_MOUSE]] Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.<ref>PMID:12925531</ref> <ref>PMID:20463020</ref> <ref>PMID:20810665</ref> <ref>PMID:21489986</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Prostaglandin-endoperoxide synthase]]
		+	[[Category: Malkowski, M G]]
		+	[[Category: Orlando, B J]]
		+	[[Category: Celebrex]]
		+	[[Category: Celecoxib]]
		+	[[Category: Cox-2]]
		+	[[Category: Coxib]]
		+	[[Category: Cyclooxygenase]]
		+	[[Category: Oxidoreductase]]

OCA at 12:27, 27 July 2016

OCA — Wed, 27 Jul 2016 12:27:05 GMT

←Older revision		Revision as of 12:27, 27 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jw1 is ON HOLD	+	The entry 5jw1 is ON HOLD until Paper Publication

	Authors: Malkowski, M.G., Orlando, B.J.		Authors: Malkowski, M.G., Orlando, B.J.

OCA: Protected "5jw1" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 13:55:30 GMT

Protected "5jw1" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:55, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jw1 is ON HOLD Authors: Malkowski, M.G., Orlando, B.J. Description: Crystal structure of Celecoxib bound to S121P murine COX-2 mutant [[Category: ...

OCA — Wed, 01 Jun 2016 13:55:29 GMT

New page: '''Unreleased structure''' The entry 5jw1 is ON HOLD Authors: Malkowski, M.G., Orlando, B.J. Description: Crystal structure of Celecoxib bound to S121P murine COX-2 mutant [[Category: ...

New page

'''Unreleased structure'''

The entry 5jw1 is ON HOLD

Authors: Malkowski, M.G., Orlando, B.J.

Description: Crystal structure of Celecoxib bound to S121P murine COX-2 mutant
[[Category: Unreleased Structures]]
[[Category: Orlando, B.J]]
[[Category: Malkowski, M.G]]