6n0d - Revision history

OCA at 14:46, 13 March 2024

OCA — Wed, 13 Mar 2024 14:46:06 GMT

←Older revision		Revision as of 14:46, 13 March 2024
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	<StructureSection load='6n0d' size='340' side='right'caption='[[6n0d]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6n0d' size='340' side='right'caption='[[6n0d]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n0d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N0D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n0d]] 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=6N0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N0D 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=K8J:4-fluorobenzene-1,2-dicarboxylic+acid'>K8J</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]] 1.453Å</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=6n0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n0d OCA], [~~http~~://pdbe.org/6n0d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n0d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n0d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n0d ProSAT]</span></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=K8J:4-fluorobenzene-1,2-dicarboxylic+acid'>K8J</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=6n0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n0d OCA], [https://pdbe.org/6n0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n0d RCSB], [https://www.ebi.ac.uk/pdbsum/6n0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n0d ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN]] Defects in TDP1 are the cause of spinocerebellar ataxia autosomal recessive with axonal neuropathy (SCAN1) [MIM:[~~http~~://omim.org/entry/607250 607250]]. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence.<ref>PMID:16141202</ref> <ref>PMID:15647511</ref> <ref>PMID:12244316</ref> <ref>PMID:17948061</ref> <ref>PMID:15920477</ref>	+	[https://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN] Defects in TDP1 are the cause of spinocerebellar ataxia autosomal recessive with axonal neuropathy (SCAN1) [MIM:[https://omim.org/entry/607250 607250]. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence.<ref>PMID:16141202</ref> <ref>PMID:15647511</ref> <ref>PMID:12244316</ref> <ref>PMID:17948061</ref> <ref>PMID:15920477</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN]] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.<ref>PMID:12023295</ref> <ref>PMID:15111055</ref> <ref>PMID:15811850</ref> <ref>PMID:16141202</ref> <ref>PMID:22822062</ref>	+	[https://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.<ref>PMID:12023295</ref> <ref>PMID:15111055</ref> <ref>PMID:15811850</ref> <ref>PMID:16141202</ref> <ref>PMID:22822062</ref>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Burke~~, T R~~]]	+	[[Category: Burke Jr TR]]
-	[[Category: Kiselev, E]]	+	[[Category: Kiselev E]]
-	[[Category: Lountos~~, G T~~]]	+	[[Category: Lountos GT]]
-	[[Category: Needle, D]]	+	[[Category: Needle D]]
-	[[Category: Pommier, Y]]	+	[[Category: Pommier Y]]
-	[[Category: Tropea~~, J E~~]]	+	[[Category: Tropea JE]]
-	[[Category: Waugh~~, D S~~]]	+	[[Category: Waugh DS]]
-	[[Category: Zhao~~, X Z]]~~	+	[[Category: Zhao XZ]]
-	~~[[Category: Anti-cancer drug design]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Fragment based drug design]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:04, 13 November 2019

OCA — Wed, 13 Nov 2019 11:04:11 GMT

←Older revision		Revision as of 11:04, 13 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6n0d ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Tdp1 catalytic domain in complex with compound XZ575==
-		+	<StructureSection load='6n0d' size='340' side='right'caption='[[6n0d]], [[Resolution\|resolution]] 1.45Å' scene=''>
-	~~Authors~~: ~~Lountos, G~~.T.~~, Zhao, X~~.Z.~~, Kiselev, E~~., ~~Tropea~~, J.E., ~~Needle, D~~., ~~Burke Jr~~., T.R., ~~Pommier, Y~~., ~~Waugh, D~~.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n0d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N0D FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~Tdp1 catalytic domain in complex~~ with ~~compound XZ575~~	+	</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=K8J:4-fluorobenzene-1,2-dicarboxylic+acid'>K8J</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6n0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n0d OCA], [http://pdbe.org/6n0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n0d RCSB], [http://www.ebi.ac.uk/pdbsum/6n0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n0d ProSAT]</span></td></tr>
-	[[~~Category~~: T.R]]	+	</table>
-	[[Category: ~~Pommier, Y~~]]	+	== Disease ==
-	[[Category: ~~Waugh~~, ~~D.S~~]]	+	[[http://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN]] Defects in TDP1 are the cause of spinocerebellar ataxia autosomal recessive with axonal neuropathy (SCAN1) [MIM:[http://omim.org/entry/607250 607250]]. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence.<ref>PMID:16141202</ref> <ref>PMID:15647511</ref> <ref>PMID:12244316</ref> <ref>PMID:17948061</ref> <ref>PMID:15920477</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN]] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.<ref>PMID:12023295</ref> <ref>PMID:15111055</ref> <ref>PMID:15811850</ref> <ref>PMID:16141202</ref> <ref>PMID:22822062</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Burke, T R]]
	[[Category: Kiselev, E]]		[[Category: Kiselev, E]]
-	[[Category: ~~Zhao~~, ~~X.Z]]~~	+	[[Category: Lountos, G T]]
-	~~[[Category: Tropea, J.E]]~~	+
-	~~[[Category: Burke Jr~~]]	+
	[[Category: Needle, D]]		[[Category: Needle, D]]
-	[[Category: ~~Lountos~~, ~~G.T~~]]	+	[[Category: Pommier, Y]]
		+	[[Category: Tropea, J E]]
		+	[[Category: Waugh, D S]]
		+	[[Category: Zhao, X Z]]
		+	[[Category: Anti-cancer drug design]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Fragment based drug design]]
		+	[[Category: Hydrolase]]

OCA at 06:44, 26 December 2018

OCA — Wed, 26 Dec 2018 06:44:22 GMT

←Older revision		Revision as of 06:44, 26 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n0d is ON HOLD	+	The entry 6n0d is ON HOLD until Paper Publication

	Authors: Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S.		Authors: Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S.
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	Description: Crystal structure of Tdp1 catalytic domain in complex with compound XZ575		Description: Crystal structure of Tdp1 catalytic domain in complex with compound XZ575
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Waugh, D.S]]
-	[[Category: Lountos, G.T]]
	[[Category: T.R]]		[[Category: T.R]]
	[[Category: Pommier, Y]]		[[Category: Pommier, Y]]
		+	[[Category: Waugh, D.S]]
	[[Category: Kiselev, E]]		[[Category: Kiselev, E]]
	[[Category: Zhao, X.Z]]		[[Category: Zhao, X.Z]]
Line 16:		Line 15:
	[[Category: Burke Jr]]		[[Category: Burke Jr]]
	[[Category: Needle, D]]		[[Category: Needle, D]]
		+	[[Category: Lountos, G.T]]

OCA: Protected "6n0d" [edit=sysop:move=sysop]

OCA — Wed, 14 Nov 2018 06:46:13 GMT

Protected "6n0d" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:46, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6n0d is ON HOLD Authors: Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S. Description: C...

OCA — Wed, 14 Nov 2018 06:46:12 GMT

New page: '''Unreleased structure''' The entry 6n0d is ON HOLD Authors: Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S. Description: C...

New page

'''Unreleased structure'''

The entry 6n0d is ON HOLD

Authors: Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Burke Jr., T.R., Pommier, Y., Waugh, D.S.

Description: Crystal structure of Tdp1 catalytic domain in complex with compound XZ575
[[Category: Unreleased Structures]]
[[Category: Waugh, D.S]]
[[Category: Lountos, G.T]]
[[Category: T.R]]
[[Category: Pommier, Y]]
[[Category: Kiselev, E]]
[[Category: Zhao, X.Z]]
[[Category: Tropea, J.E]]
[[Category: Burke Jr]]
[[Category: Needle, D]]