5jix - Revision history

OCA at 18:53, 20 September 2023

2023-09-20T18:53:40Z

←Older revision		Revision as of 18:53, 20 September 2023
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	==PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP==		==PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP==
-	<StructureSection load='5jix' size='340' side='right' caption='[[5jix]], [[Resolution\|resolution]] 1.47Å' scene=''>	+	<StructureSection load='5jix' size='340' side='right'caption='[[5jix]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jix]] is a 1 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=5JIX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jix]] is a 1 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=5JIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JIX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6J7:2-AMINO-8-BROMO-9-[(2R,4AR,6R,7R,7AS)-2,7-DIHYDROXY-2-OXOTETRAHYDRO-2H,4H-2LAMBDA~5~-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-6-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>6J7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</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]] 1.47Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jiz\|5jiz]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6J7:2-AMINO-8-BROMO-9-[(2R,4AR,6R,7R,7AS)-2,7-DIHYDROXY-2-OXOTETRAHYDRO-2H,4H-2LAMBDA~5~-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-6-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>6J7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PRKG2, PRKGR2 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [https://pdbe.org/5jix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [https://www.ebi.ac.uk/pdbsum/5jix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix 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/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.12 2.7.11.12] </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=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [~~http~~://pdbe.org/5jix PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jix PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KGP2_HUMAN KGP2_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Large Structures]]
-	[[Category: Campbell~~, J C~~]]	+	[[Category: Campbell JC]]
-	[[Category: Kim~~, C W]]~~	+	[[Category: Kim CW]]
-	~~[[Category: Cyclic gmp-dependent protein kinase type ii~~]]	+

OCA at 12:54, 6 November 2017

2017-11-06T12:54:43Z

←Older revision		Revision as of 12:54, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5jix' size='340' side='right' caption='[[5jix]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='5jix' size='340' side='right' caption='[[5jix]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jix]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jix]] is a 1 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=5JIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JIX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6J7:2-AMINO-8-BROMO-9-[(2R,4AR,6R,7R,7AS)-2,7-DIHYDROXY-2-OXOTETRAHYDRO-2H,4H-2LAMBDA~5~-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-6-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>6J7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6J7:2-AMINO-8-BROMO-9-[(2R,4AR,6R,7R,7AS)-2,7-DIHYDROXY-2-OXOTETRAHYDRO-2H,4H-2LAMBDA~5~-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-6-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>6J7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jiz\|5jiz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jiz\|5jiz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PRKG2, PRKGR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.12 2.7.11.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.12 2.7.11.12] </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=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [http://pdbe.org/5jix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [http://www.ebi.ac.uk/pdbsum/5jix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix ProSAT]</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=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [http://pdbe.org/5jix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [http://www.ebi.ac.uk/pdbsum/5jix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Campbell, J C]]		[[Category: Campbell, J C]]
	[[Category: Kim, C W]]		[[Category: Kim, C W]]
	[[Category: Cyclic gmp-dependent protein kinase type ii]]		[[Category: Cyclic gmp-dependent protein kinase type ii]]

OCA at 10:58, 24 August 2017

2017-08-24T10:58:38Z

←Older revision		Revision as of 10:58, 24 August 2017
Line 9:		Line 9:
	<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=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [http://pdbe.org/5jix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [http://www.ebi.ac.uk/pdbsum/5jix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix ProSAT]</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=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [http://pdbe.org/5jix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [http://www.ebi.ac.uk/pdbsum/5jix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cyclic GMP analogs, 8-Br, 8-pCPT, and PET-cGMP, have been widely used for characterizing cellular functions of cGMP-dependent protein kinase (PKG) I and II isotypes. However, interpreting results obtained using these analogs has been difficult due to their low isotype specificity. Additionally, each isotype has two binding sites with different cGMP affinities and analog selectivities, making understanding the molecular basis for isotype specificity of these compounds even more challenging. To determine isotype specificity of cGMP analogs and their structural basis, we generated the full-length regulatory domains of PKG I and II isotypes with each binding site disabled, determined their affinities for these analogs, and obtained cocrystal structures of both isotypes bound with cGMP analogs. Our affinity and activation measurements show that PET-cGMP is most selective for PKG I, whereas 8-pCPT-cGMP is most selective for PKG II. Our structures of cyclic nucleotide binding (CNB) domains reveal that the B site of PKG I is more open and forms a unique pi/pi interaction through Arg285 at beta4 with the PET moiety, whereas the A site of PKG II has a larger beta5/beta6 pocket that can better accommodate the bulky 8-pCPT moiety. Our structural and functional results explain the selectivity of these analogs for each PKG isotype and provide a starting point for the rational design of isotype selective activators.
		+
		+	Structural Basis of Analog Specificity in PKG I and II.,Campbell JC, Henning P, Franz E, Sankaran B, Herberg FW, Kim C ACS Chem Biol. 2017 Aug 22. doi: 10.1021/acschembio.7b00369. PMID:28793191<ref>PMID:28793191</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jix" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:07, 4 May 2017

2017-05-04T13:07:48Z

←Older revision		Revision as of 13:07, 4 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5jix is ON HOLD until Paper Publication~~	+	==PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP==
-		+	<StructureSection load='5jix' size='340' side='right' caption='[[5jix]], [[Resolution\|resolution]] 1.47Å' scene=''>
-	~~Authors: Campbell, J.C., Kim, C.W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jix]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JIX FirstGlance]. <br>
-	~~Description:~~ PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6J7:2-AMINO-8-BROMO-9-[(2R,4AR,6R,7R,7AS)-2,7-DIHYDROXY-2-OXOTETRAHYDRO-2H,4H-2LAMBDA~5~-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-6-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>6J7</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jiz\|5jiz]]</td></tr>
-	[[Category: Campbell, J.C]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.12 2.7.11.12] </span></td></tr>
-	[[Category: Kim, C.W]]	+	<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=5jix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jix OCA], [http://pdbe.org/5jix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jix RCSB], [http://www.ebi.ac.uk/pdbsum/5jix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jix ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Transferase]]
		+	[[Category: Campbell, J C]]
		+	[[Category: Kim, C W]]
		+	[[Category: Cyclic gmp-dependent protein kinase type ii]]

OCA at 09:54, 9 March 2017

2017-03-09T09:54:01Z

←Older revision		Revision as of 09:54, 9 March 2017
Line 7:		Line 7:
	Description: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP		Description: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kim, C.W]]
	[[Category: Campbell, J.C]]		[[Category: Campbell, J.C]]
		+	[[Category: Kim, C.W]]

OCA at 13:28, 1 June 2016

2016-06-01T13:28:15Z

←Older revision		Revision as of 13:28, 1 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Campbell, J.C., Kim, C.W.		Authors: Campbell, J.C., Kim, C.W.

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

2016-05-11T02:08:39Z

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

←Older revision

Revision as of 02:08, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jix is ON HOLD Authors: Campbell, J.C., Kim, C.W. Description: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex wi...

2016-05-11T02:08:38Z

New page: '''Unreleased structure''' The entry 5jix is ON HOLD Authors: Campbell, J.C., Kim, C.W. Description: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex wi...

New page

'''Unreleased structure'''

The entry 5jix is ON HOLD

Authors: Campbell, J.C., Kim, C.W.

Description: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP
[[Category: Unreleased Structures]]
[[Category: Kim, C.W]]
[[Category: Campbell, J.C]]