6j0h - Revision history

OCA at 10:26, 15 November 2023

OCA — Wed, 15 Nov 2023 10:26:27 GMT

←Older revision		Revision as of 10:26, 15 November 2023
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	<StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J0H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J0H FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.52Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [https://pdbe.org/6j0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [https://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h 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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [https://pdbe.org/6j0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [https://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hou, M H~~]]	+	[[Category: Streptomyces sp]]
-	[[Category: ~~Satange, R B~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Actinomycin d~~]]	+	[[Category: Hou MH]]
-	[[Category: ~~Base flip out]]~~	+	[[Category: Satange RB]]
-	~~[[Category: Dna kink]]~~	+
-	~~[[Category: Dna-antibiotic complex]]~~	+
-	~~[[Category: Drug-dna complex]]~~	+
-	~~[[Category: Mismatch dna~~]]	+

OCA at 07:15, 9 March 2022

OCA — Wed, 09 Mar 2022 07:15:28 GMT

←Older revision		Revision as of 07:15, 9 March 2022
Line 3:		Line 3:
	<StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6J0H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J0H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [~~http~~://pdbe.org/6j0h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h 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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [https://pdbe.org/6j0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [https://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:34, 21 August 2019

OCA — Wed, 21 Aug 2019 06:34:30 GMT

←Older revision		Revision as of 06:34, 21 August 2019
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	<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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [http://pdbe.org/6j0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [http://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h 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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [http://pdbe.org/6j0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [http://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn-syn, water mediated anti-syn and syn-syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5' intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
		+
		+	Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.,Satange R, Chuang CY, Neidle S, Hou MH Nucleic Acids Res. 2019 Jul 30. pii: 5541096. doi: 10.1093/nar/gkz653. PMID:31361900<ref>PMID:31361900</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6j0h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:12, 24 July 2019

OCA — Wed, 24 Jul 2019 06:12:16 GMT

←Older revision		Revision as of 06:12, 24 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6j0h is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Actinomycin D- d(TTGGCGAA) complex==
-		+	<StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution\|resolution]] 1.52Å' scene=''>
-	~~Authors~~: ~~Satange~~, R.B., ~~Hou~~, M.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J0H FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Actinomycin D~~-~~d(TTGGCGAA) complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr>
-	[[Category: Satange, R.B]]	+	<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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [http://pdbe.org/6j0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [http://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h ProSAT]</span></td></tr>
-	[[Category: ~~Hou, M.H~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hou, M H]]
		+	[[Category: Satange, R B]]
		+	[[Category: Actinomycin d]]
		+	[[Category: Base flip out]]
		+	[[Category: Dna kink]]
		+	[[Category: Dna-antibiotic complex]]
		+	[[Category: Drug-dna complex]]
		+	[[Category: Mismatch dna]]

OCA at 07:10, 13 February 2019

OCA — Wed, 13 Feb 2019 07:10:52 GMT

←Older revision		Revision as of 07:10, 13 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6j0h is ON HOLD	+	The entry 6j0h is ON HOLD until Paper Publication

	Authors: Satange, R.B., Hou, M.H.		Authors: Satange, R.B., Hou, M.H.
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	Description: Crystal structure of Actinomycin D-d(TTGGCGAA) complex		Description: Crystal structure of Actinomycin D-d(TTGGCGAA) complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hou, M.H]]
	[[Category: Satange, R.B]]		[[Category: Satange, R.B]]
		+	[[Category: Hou, M.H]]

OCA: Protected "6j0h" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2019 04:50:32 GMT

Protected "6j0h" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:50, 2 January 2019

OCA: New page: '''Unreleased structure''' The entry 6j0h is ON HOLD Authors: Satange, R.B., Hou, M.H. Description: Crystal structure of Actinomycin D-d(TTGGCGAA) complex [[Category: Unreleased Struct...

OCA — Wed, 02 Jan 2019 04:50:30 GMT

New page: '''Unreleased structure''' The entry 6j0h is ON HOLD Authors: Satange, R.B., Hou, M.H. Description: Crystal structure of Actinomycin D-d(TTGGCGAA) complex [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 6j0h is ON HOLD

Authors: Satange, R.B., Hou, M.H.

Description: Crystal structure of Actinomycin D-d(TTGGCGAA) complex
[[Category: Unreleased Structures]]
[[Category: Hou, M.H]]
[[Category: Satange, R.B]]