5een - Revision history

OCA at 06:23, 5 July 2023

OCA — Wed, 05 Jul 2023 06:23:21 GMT

←Older revision		Revision as of 06:23, 5 July 2023
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	<StructureSection load='5een' size='340' side='right'caption='[[5een]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='5een' size='340' side='right'caption='[[5een]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5een]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5een]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EEN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OG:BELINOSTAT'>5OG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.861Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5edu\|5edu]]~~, [[~~5eef~~\|~~5eef]], [[5eei\|5eei]], [[5eek\|5eek]], [[5eem\|5eem]], [[5ef7\|5ef7]], [[5ef8\|5ef8]], [[5efb\|5efb]], [[5efg\|5efg]], [[5efh\|5efh]], [[5efj\|5efj]], [[5efk\|5efk]], [[5efn\|5efn~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5OG:BELINOSTAT'>5OG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~hdac6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=7955 Brachidanio rerio])</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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [https://pdbe.org/5een PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [https://www.ebi.ac.uk/pdbsum/5een PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5een 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/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98]~~ </~~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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [~~http~~://pdbe.org/5een PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5een PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5een ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	~~[[Category: Histone deacetylase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christianson~~, D W~~]]	+	[[Category: Christianson DW]]
-	[[Category: Hai, Y]]	+	[[Category: Hai Y]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 11:32, 25 December 2019

OCA — Wed, 25 Dec 2019 11:32:27 GMT

←Older revision		Revision as of 11:32, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat==		==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat==
-	<StructureSection load='5een' size='340' side='right' caption='[[5een]], [[Resolution\|resolution]] 1.86Å' scene=''>	+	<StructureSection load='5een' size='340' side='right'caption='[[5een]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5een]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5een]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EEN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OG:BELINOSTAT'>5OG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OG:BELINOSTAT'>5OG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5edu\|5edu]], [[5eef\|5eef]], [[5eei\|5eei]], [[5eek\|5eek]], [[5eem\|5eem]], [[5ef7\|5ef7]], [[5ef8\|5ef8]], [[5efb\|5efb]], [[5efg\|5efg]], [[5efh\|5efh]], [[5efj\|5efj]], [[5efk\|5efk]], [[5efn\|5efn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5edu\|5edu]], [[5eef\|5eef]], [[5eei\|5eei]], [[5eek\|5eek]], [[5eem\|5eem]], [[5ef7\|5ef7]], [[5ef8\|5ef8]], [[5efb\|5efb]], [[5efg\|5efg]], [[5efh\|5efh]], [[5efj\|5efj]], [[5efk\|5efk]], [[5efn\|5efn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hdac6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [http://pdbe.org/5een PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [http://www.ebi.ac.uk/pdbsum/5een PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5een 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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [http://pdbe.org/5een PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [http://www.ebi.ac.uk/pdbsum/5een PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5een ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5een" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5een" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
		+	[[Category: Large Structures]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]
	[[Category: Hai, Y]]		[[Category: Hai, Y]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 08:29, 10 August 2016

OCA — Wed, 10 Aug 2016 08:29:07 GMT

←Older revision		Revision as of 08:29, 10 August 2016
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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [http://pdbe.org/5een PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [http://www.ebi.ac.uk/pdbsum/5een PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5een 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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [http://pdbe.org/5een PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [http://www.ebi.ac.uk/pdbsum/5een PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5een ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Histone deacetylase 6 (HDAC6) is a critical target for drug design because of its role in oncogenic transformation and cancer metastasis, and is unique among all histone deacetylases in that it contains tandem catalytic domains designated CD1 and CD2. We now report the crystal structures of CD2 from Homo sapiens HDAC6 and of CD1 and CD2 from Danio rerio HDAC6. We correlated these structures with activity measurements using 13 different substrates. The catalytic activity of CD2 from both species exhibited broad substrate specificity, whereas that of CD1 was highly specific for substrates bearing C-terminal acetyllysine residues. Crystal structures of substrate complexes yielded unprecedented snapshots of the catalytic mechanism. Additionally, crystal structures of complexes with eight different inhibitors, including belinostat and panobinostat (currently used in cancer chemotherapy), the macrocyclic tetrapeptide HC toxin, and the HDAC6-specific inhibitor N-hydroxy-4-(2-((2-hydroxyethyl)(phenyl)amino)-2-oxoethyl)benzamide, revealed surprising new insight regarding changes in Zn2+ coordination and isozyme-specific inhibition.
		+
		+	Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.,Hai Y, Christianson DW Nat Chem Biol. 2016 Jul 25. doi: 10.1038/nchembio.2134. PMID:27454933<ref>PMID:27454933</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5een" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:38, 27 July 2016

OCA — Wed, 27 Jul 2016 15:38:21 GMT

←Older revision		Revision as of 15:38, 27 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5een is ON HOLD until Paper Publication~~	+	==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat==
-		+	<StructureSection load='5een' size='340' side='right' caption='[[5een]], [[Resolution\|resolution]] 1.86Å' scene=''>
-	~~Authors: Hai, Y., Christianson, D.W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5een]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EEN FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OG:BELINOSTAT'>5OG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5edu\|5edu]], [[5eef\|5eef]], [[5eei\|5eei]], [[5eek\|5eek]], [[5eem\|5eem]], [[5ef7\|5ef7]], [[5ef8\|5ef8]], [[5efb\|5efb]], [[5efg\|5efg]], [[5efh\|5efh]], [[5efj\|5efj]], [[5efk\|5efk]], [[5efn\|5efn]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=5een FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5een OCA], [http://pdbe.org/5een PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5een RCSB], [http://www.ebi.ac.uk/pdbsum/5een PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5een ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone deacetylase]]
		+	[[Category: Christianson, D W]]
	[[Category: Hai, Y]]		[[Category: Hai, Y]]
-	[[Category: ~~Christianson, D.W~~]]	+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 14:11, 26 February 2016

OCA — Fri, 26 Feb 2016 14:11:33 GMT

←Older revision		Revision as of 14:11, 26 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Hai, Y., Christianson, D.W.		Authors: Hai, Y., Christianson, D.W.

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

OCA — Tue, 01 Dec 2015 02:44:25 GMT

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

←Older revision

Revision as of 02:44, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5een is ON HOLD Authors: Hai, Y., Christianson, D.W. Description: Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in comp...

OCA — Tue, 01 Dec 2015 02:44:24 GMT

New page: '''Unreleased structure''' The entry 5een is ON HOLD Authors: Hai, Y., Christianson, D.W. Description: Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in comp...

New page

'''Unreleased structure'''

The entry 5een is ON HOLD

Authors: Hai, Y., Christianson, D.W.

Description: Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat
[[Category: Unreleased Structures]]
[[Category: Hai, Y]]
[[Category: Christianson, D.W]]