3u08 - Revision history

OCA at 10:16, 1 March 2024

OCA — Fri, 01 Mar 2024 10:16:22 GMT

←Older revision		Revision as of 10:16, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U08 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U08 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=D63:4~~-~~(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.25Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height~~: ~~3em;~~'>~~[[3u05\|3u05]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D63:4-(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [https://pdbe.org/3u08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [https://www.ebi.ac.uk/pdbsum/3u08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u08 ProSAT]</span></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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [https://pdbe.org/3u08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [https://www.ebi.ac.uk/pdbsum/3u08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u08 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
-
-	Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.,Wei D, Wilson WD, Neidle S J Am Chem Soc. 2013 Jan 30;135(4):1369-77. doi: 10.1021/ja308952y. Epub 2013 Jan , 16. PMID:23276263<ref>PMID:23276263</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3u08" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Neidle, S]]	+	[[Category: Neidle S]]
-	[[Category: Wei~~, D G]]~~	+	[[Category: Wei DG]]
-	~~[[Category: Db1963]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna minor groove-ligand binder]]~~	+
-	~~[[Category: Double helix~~]]	+

OCA at 05:52, 13 July 2022

OCA — Wed, 13 Jul 2022 05:52:24 GMT

←Older revision		Revision as of 05:52, 13 July 2022
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	==Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution==		==Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution==
-	<StructureSection load='3u08' size='340' side='right' caption='[[3u08]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='3u08' size='340' side='right'caption='[[3u08]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3U08 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U08 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D63:4-(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D63:4-(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u05\|3u05]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3u05\|3u05]]</div></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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [~~http~~://pdbe.org/3u08 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3u08 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3u08 ProSAT]</span></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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [https://pdbe.org/3u08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [https://www.ebi.ac.uk/pdbsum/3u08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u08 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Neidle, S]]		[[Category: Neidle, S]]
	[[Category: Wei, D G]]		[[Category: Wei, D G]]

OCA at 21:42, 5 August 2016

OCA — Fri, 05 Aug 2016 21:42:42 GMT

←Older revision		Revision as of 21:42, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution==		==Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution==
	<StructureSection load='3u08' size='340' side='right' caption='[[3u08]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='3u08' size='340' side='right' caption='[[3u08]], [[Resolution\|resolution]] 1.25Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D63:4-(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D63:4-(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u05\|3u05]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u05\|3u05]]</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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [http://www.ebi.ac.uk/pdbsum/3u08 PDBsum]</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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [http://pdbe.org/3u08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [http://www.ebi.ac.uk/pdbsum/3u08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u08 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3u08" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:08, 21 December 2014

OCA — Sun, 21 Dec 2014 17:08:58 GMT

←Older revision		Revision as of 17:08, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3u08\| PDB=3u08 \| SCENE= }}~~	+	==Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution==
-	===Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution===	+	<StructureSection load='3u08' size='340' side='right' caption='[[3u08]], [[Resolution\|resolution]] 1.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23276263}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U08 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D63:4-(5-CARBAMIMIDOYL-1H-BENZIMIDAZOL-2-YL)BIPHENYL-4-CARBOXAMIDE'>D63</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u05\|3u05]]</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=3u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u08 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u08 RCSB], [http://www.ebi.ac.uk/pdbsum/3u08 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.

-	~~==About this Structure==~~	+	Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.,Wei D, Wilson WD, Neidle S J Am Chem Soc. 2013 Jan 30;135(4):1369-77. doi: 10.1021/ja308952y. Epub 2013 Jan , 16. PMID:23276263<ref>PMID:23276263</ref>
-	~~[[3u08]]~~ is a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3U08 OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023276263</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Neidle, S.]]	+	== References ==
-	[[Category: Wei, D G.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Neidle, S]]
		+	[[Category: Wei, D G]]
	[[Category: Db1963]]		[[Category: Db1963]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna minor groove-ligand binder]]		[[Category: Dna minor groove-ligand binder]]
	[[Category: Double helix]]		[[Category: Double helix]]

OCA at 08:28, 8 January 2014

OCA — Wed, 08 Jan 2014 08:28:04 GMT

←Older revision		Revision as of 08:28, 8 January 2014
Line 1:		Line 1:
-	[[Image:3u08.jpg\|left\|200px]]
-
	{{STRUCTURE_3u08\| PDB=3u08 \| SCENE= }}		{{STRUCTURE_3u08\| PDB=3u08 \| SCENE= }}
-
	===Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution===		===Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution===
-		+	{{ABSTRACT_PUBMED_23276263}}

	==About this Structure==		==About this Structure==
	[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA].		[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023276263</ref><references group="xtra"/><references/>
	[[Category: Neidle, S.]]		[[Category: Neidle, S.]]
	[[Category: Wei, D G.]]		[[Category: Wei, D G.]]

OCA at 05:19, 12 September 2012

OCA — Wed, 12 Sep 2012 05:19:05 GMT

←Older revision		Revision as of 05:19, 12 September 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3u08.jpg\|left\|200px]]

-	~~The entry~~ 3u08 ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3u08\| PDB=3u08 \| SCENE= }}

-	~~Authors: Wei,~~ D.~~G., Neidle, S.~~	+	===Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution===

-	~~Description: Crystal~~ structure ~~of DB1963~~-D~~(CGCGAATTCGCG)2 complex at 1~~.~~25 A resolution~~	+
		+	==About this Structure==
		+	[[3u08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U08 OCA].
		+	[[Category: Neidle, S.]]
		+	[[Category: Wei, D G.]]
		+	[[Category: Db1963]]
		+	[[Category: Dna]]
		+	[[Category: Dna minor groove-ligand binder]]
		+	[[Category: Double helix]]

OCA at 08:46, 30 October 2011

OCA — Sun, 30 Oct 2011 08:46:58 GMT

←Older revision		Revision as of 08:46, 30 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3u08 is ON HOLD	+	The entry 3u08 is ON HOLD until Paper Publication

	Authors: Wei, D.G., Neidle, S.		Authors: Wei, D.G., Neidle, S.

	Description: Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution		Description: Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution

OCA: Protected "3u08" [edit=sysop:move=sysop]

OCA — Wed, 05 Oct 2011 06:15:16 GMT

Protected "3u08" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:15, 5 October 2011

OCA: New page: '''Unreleased structure''' The entry 3u08 is ON HOLD Authors: Wei, D.G., Neidle, S. Description: Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution

OCA — Wed, 05 Oct 2011 06:15:15 GMT

New page: '''Unreleased structure''' The entry 3u08 is ON HOLD Authors: Wei, D.G., Neidle, S. Description: Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution

New page

'''Unreleased structure'''

The entry 3u08 is ON HOLD

Authors: Wei, D.G., Neidle, S.

Description: Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution