5f6u - Revision history

OCA at 06:40, 19 July 2023

2023-07-19T06:40:21Z

←Older revision		Revision as of 06:40, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5f6u' size='340' side='right'caption='[[5f6u]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5f6u' size='340' side='right'caption='[[5f6u]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f6u]] 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=5F6U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5F6U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f6u]] 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=5F6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F6U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=5VK:ETHYL+3~~-[~~4-(2-HYDROXYPHENYL)-3-OXIDANYL-PHENYL~~]~~PROPANOATE'>5VK</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]] 1.552Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5f6d\|5f6d]], [[5f6e\|5f6e]], [[5f6v\|5f6v]], [[5f5w\|5f5w]], [[5f6x\|5f6x]], [[5f6y\|5f6y]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5VK:ETHYL+3-[4-(2-HYDROXYPHENYL)-3-OXIDANYL-PHENYL]PROPANOATE'>5VK</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><b>[~~[Gene\|Gene:~~]~~]</b~~></td>~~<td class="sblockDat">UBE2I, UBC9, UBCE9 ([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=5f6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6u OCA], [https://pdbe.org/5f6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f6u RCSB], [https://www.ebi.ac.uk/pdbsum/5f6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6u 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=5f6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6u OCA], [~~http~~://pdbe.org/5f6u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f6u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f6u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6u ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>	+	[https://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dahlhauser, S]]	+	[[Category: Dahlhauser S]]
-	[[Category: Hewitt~~, W M~~]]	+	[[Category: Hewitt WM]]
-	[[Category: Lountos~~, G T~~]]	+	[[Category: Lountos GT]]
-	[[Category: Ma, B]]	+	[[Category: Ma B]]
-	[[Category: Needle, D]]	+	[[Category: Needle D]]
-	[[Category: Nussinov, R]]	+	[[Category: Nussinov R]]
-	[[Category: Saunders~~, L B~~]]	+	[[Category: Saunders LB]]
-	[[Category: Schneekloth~~, J S.Jr~~]]	+	[[Category: Schneekloth JSJr]]
-	[[Category: Tropea~~, J E~~]]	+	[[Category: Tropea JE]]
-	[[Category: Waugh~~, D S~~]]	+	[[Category: Waugh DS]]
-	[[Category: Wei, G]]	+	[[Category: Wei G]]
-	[[Category: Zhan, C]]	+	[[Category: Zhan C]]
-	[[Category: Zlotkowski, Z]]	+	[[Category: Zlotkowski Z]]
-	~~[[Category: Drug discovery]]~~	+
-	~~[[Category: Ligase-ligase inhibitor complex]]~~	+
-	~~[[Category: Sumoylation]]~~	+
-	~~[[Category: Ubc9~~]]	+

OCA at 08:02, 29 April 2020

2020-04-29T08:02:05Z

←Older revision		Revision as of 08:02, 29 April 2020
Line 1:		Line 1:

	==Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)==		==Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)==
-	<StructureSection load='5f6u' size='340' side='right' caption='[[5f6u]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5f6u' size='340' side='right'caption='[[5f6u]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f6u]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F6U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F6U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f6u]] 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=5F6U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5F6U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5VK:ETHYL+3-[4-(2-HYDROXYPHENYL)-3-OXIDANYL-PHENYL]PROPANOATE'>5VK</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5VK:ETHYL+3-[4-(2-HYDROXYPHENYL)-3-OXIDANYL-PHENYL]PROPANOATE'>5VK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f6d\|5f6d]], [[5f6e\|5f6e]], [[5f6v\|5f6v]], [[5f5w\|5f5w]], [[5f6x\|5f6x]], [[5f6y\|5f6y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f6d\|5f6d]], [[5f6e\|5f6e]], [[5f6v\|5f6v]], [[5f5w\|5f5w]], [[5f6x\|5f6x]], [[5f6y\|5f6y]]</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=5f6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6u OCA], [http://pdbe.org/5f6u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f6u RCSB], [http://www.ebi.ac.uk/pdbsum/5f6u PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UBE2I, UBC9, UBCE9 ([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://proteopedia.org/fgij/fg.htm?mol=5f6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6u OCA], [http://pdbe.org/5f6u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f6u RCSB], [http://www.ebi.ac.uk/pdbsum/5f6u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5f6u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f6u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[SUMO conjugating enzyme Ubc9\|SUMO conjugating enzyme Ubc9]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Dahlhauser, S]]		[[Category: Dahlhauser, S]]
	[[Category: Hewitt, W M]]		[[Category: Hewitt, W M]]

OCA at 16:10, 10 May 2016

2016-05-10T16:10:58Z

←Older revision		Revision as of 16:10, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5f6u is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)==
		+	<StructureSection load='5f6u' size='340' side='right' caption='[[5f6u]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5f6u]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F6U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F6U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5VK:ETHYL+3-[4-(2-HYDROXYPHENYL)-3-OXIDANYL-PHENYL]PROPANOATE'>5VK</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f6d\|5f6d]], [[5f6e\|5f6e]], [[5f6v\|5f6v]], [[5f5w\|5f5w]], [[5f6x\|5f6x]], [[5f6y\|5f6y]]</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=5f6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6u OCA], [http://pdbe.org/5f6u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f6u RCSB], [http://www.ebi.ac.uk/pdbsum/5f6u PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBC9_HUMAN UBC9_HUMAN]] Accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3 and SUMO4 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2 or CBX4. Can catalyze the formation of poly-SUMO chains. Necessary for sumoylation of FOXL2 and KAT5. Essential for nuclear architecture and chromosome segregation.<ref>PMID:8668529</ref> <ref>PMID:11451954</ref> <ref>PMID:15809060</ref> <ref>PMID:19744555</ref> <ref>PMID:19638400</ref> <ref>PMID:17466333</ref> <ref>PMID:20077568</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small-molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X-ray crystallographic screen was used to identify two distinct small-molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9-5.8 mm. Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand-induced rigidification of Ubc9 as a mechanism of inhibition.

-	~~Authors: Lountos, G.T~~., Hewitt, ~~W.M.~~, Zlotkowski~~, Z.~~, Dahlhauser~~, S.~~, Saunders~~, L.B.~~, Needle, D., Tropea~~, J.E.~~, Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth~~, J~~.S.Jr., ~~Waugh, D.S~~.	+	Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.,Hewitt WM, Lountos GT, Zlotkowski K, Dahlhauser SD, Saunders LB, Needle D, Tropea JE, Zhan C, Wei G, Ma B, Nussinov R, Waugh DS, Schneekloth JS Jr Angew Chem Int Ed Engl. 2016 May 4;55(19):5703-7. doi: 10.1002/anie.201511351., Epub 2016 Apr 1. PMID:27038327<ref>PMID:27038327</ref>

-	~~Description: Crystal Structure~~ of ~~Ubc9 (K48A/K49A~~/~~E54A) complexed with Fragment 8 (JSS190B146)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Ma, B]]~~	+	<div class="pdbe-citations 5f6u" style="background-color:#fffaf0;"></div>
-	~~[[Category: Hewitt, W.M]]~~	+	== References ==
-	~~[[Category: Wei, G]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Dahlhauser, S]]		[[Category: Dahlhauser, S]]
-	[[Category: ~~Zlotkowski~~, Z]]	+	[[Category: Hewitt, W M]]
		+	[[Category: Lountos, G T]]
		+	[[Category: Ma, B]]
		+	[[Category: Needle, D]]
	[[Category: Nussinov, R]]		[[Category: Nussinov, R]]
-	[[Category: ~~Tropea~~, ~~J.E~~]]	+	[[Category: Saunders, L B]]
-	[[Category: ~~Saunders~~, L.B]]	+	[[Category: Schneekloth, J S.Jr]]
-	[[Category: ~~Schneekloth~~, J~~.S.Jr~~]]	+	[[Category: Tropea, J E]]
-	[[Category: Waugh, D.S]]	+	[[Category: Waugh, D S]]
-	[[Category: ~~Lountos~~, G.T]]	+	[[Category: Wei, G]]
	[[Category: Zhan, C]]		[[Category: Zhan, C]]
-	[[Category: ~~Needle~~, D]]	+	[[Category: Zlotkowski, Z]]
		+	[[Category: Drug discovery]]
		+	[[Category: Ligase-ligase inhibitor complex]]
		+	[[Category: Sumoylation]]
		+	[[Category: Ubc9]]

OCA at 11:34, 2 March 2016

2016-03-02T11:34:11Z

←Older revision		Revision as of 11:34, 2 March 2016
Line 5:		Line 5:
	Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.		Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

-	Description: Crystal Structure of ~~human~~ Ubc9 (K48A/K49A/E54A) complexed with Fragment 7 (JSS190B146)	+	Description: Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ma, B]]		[[Category: Ma, B]]

OCA at 17:55, 13 January 2016

2016-01-13T17:55:24Z

←Older revision		Revision as of 17:55, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f6u is ON HOLD	+	The entry 5f6u is ON HOLD until Paper Publication

	Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.		Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

OCA: Protected "5f6u" [edit=sysop:move=sysop]

2015-12-16T12:38:03Z

Protected "5f6u" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:38, 16 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f6u is ON HOLD Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., M...

2015-12-16T12:38:02Z

New page: '''Unreleased structure''' The entry 5f6u is ON HOLD Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., M...

New page

'''Unreleased structure'''

The entry 5f6u is ON HOLD

Authors: Lountos, G.T., Hewitt, W.M., Zlotkowski, Z., Dahlhauser, S., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B., Nussinov, R., Schneekloth, J.S.Jr., Waugh, D.S.

Description: Crystal Structure of human Ubc9 (K48A/K49A/E54A) complexed with Fragment 7 (JSS190B146)
[[Category: Unreleased Structures]]
[[Category: Ma, B]]
[[Category: Hewitt, W.M]]
[[Category: Wei, G]]
[[Category: Dahlhauser, S]]
[[Category: Zlotkowski, Z]]
[[Category: Nussinov, R]]
[[Category: Tropea, J.E]]
[[Category: Saunders, L.B]]
[[Category: Schneekloth, J.S.Jr]]
[[Category: Waugh, D.S]]
[[Category: Lountos, G.T]]
[[Category: Zhan, C]]
[[Category: Needle, D]]