474d - Revision history

OCA at 10:40, 1 March 2024

2024-03-01T10:40:13Z

←Older revision		Revision as of 10:40, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=474D FirstGlance]. <br>		<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=474D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NT:NETROPSIN'>NT</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]] 2.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DI:~~2-DEOXYINOSINE-5-MONOPHOSPHATE~~'>DI</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=NT:NETROPSIN'>NT</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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [https://pdbe.org/474d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [https://www.ebi.ac.uk/pdbsum/474d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=474d 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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [https://pdbe.org/474d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [https://www.ebi.ac.uk/pdbsum/474d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=474d ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Netropsin is bound to the DNA decamer d(CCCCCIIIII)2, the C-4 bromo derivative d(CCCBr5CCIIIII)2and the C-2 bromo derivative d(CBr5CCCCIIIII)2in a novel 2:1 mode. Complexes of the native decamer and the C-4 bromo derivative are isomorphous, space group P1, unit cell dimensions a = 32.56 A (32.66), b = 32.59 A (32.77), c = 37.64 A (37.71), alpha = 86.30 degrees (86.01 degrees), beta = 84.50 degrees (84.37 degrees), gamma = 68.58 degrees (68.90 degrees) with two independent molecules (A and B) in the asymmetric unit (values in parentheses are for the derivative). The C-2 bromo derivative is hexagonal P61, unit cell dimensions a = b = 32.13 A, c = 143.92, gamma = 120 degrees with one molecule in the asymmetric unit. The structures were solved by the molecular replacement method. The novelty of the structures is that there are two netropsins bound end-to-end in the minor groove of each B-DNA decamer which has nearly a complete turn. The netropsins are held by hydrogen bonding interactions to the base atoms and by sandwiching van der Waal's interactions from the sugar-phosphate backbones of the double helix similar to every other drug.DNA complex. Each netropsin molecule spans approximately 5 bp. The netropsins refined with their guanidinium heads facing each other at the center, although an orientational disorder for the netropsins cannot be excluded. The amidinium ends stretch out toward the junctions and bind to the adjacent duplexes in the columns of stacked symmetry-related complexes. Both cationic ends of netropsin are bridged by water molecules in one of the independent molecules (molecule A) of the triclinic structures and also the hexagonal structure to form pseudo-continuous drug.decamer helices.
-
-	A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2.,Chen X, Mitra SN, Rao ST, Sekar K, Sundaralingam M Nucleic Acids Res. 1998 Dec 1;26(23):5464-71. PMID:9826773<ref>PMID:9826773</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 474d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, X]]	+	[[Category: Chen X]]
-	[[Category: Rao~~, S T~~]]	+	[[Category: Rao ST]]
-	[[Category: Sekar, K]]	+	[[Category: Sekar K]]
-	[[Category: Sundaralingam, M]]	+	[[Category: Sundaralingam M]]
-	~~[[Category: B-dna/rna]]~~	+
-	~~[[Category: Complexed with drug]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double drug in minor groove]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Mismatched]]~~	+
-	~~[[Category: Modified~~]]	+

OCA at 07:35, 18 August 2022

2022-08-18T07:35:08Z

←Older revision		Revision as of 07:35, 18 August 2022
Line 3:		Line 3:
	<StructureSection load='474d' size='340' side='right'caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='474d' size='340' side='right'caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=474D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=474D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [~~http~~://pdbe.org/474d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/474d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=474d 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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [https://pdbe.org/474d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [https://www.ebi.ac.uk/pdbsum/474d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=474d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:09, 1 January 2020

2020-01-01T13:09:55Z

←Older revision		Revision as of 13:09, 1 January 2020
Line 1:		Line 1:

	==A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2==		==A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2==
-	<StructureSection load='474d' size='340' side='right' caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='474d' size='340' side='right'caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=474D FirstGlance]. <br>		<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=474D FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chen, X]]		[[Category: Chen, X]]
	[[Category: Rao, S T]]		[[Category: Rao, S T]]

OCA at 09:29, 11 August 2016

2016-08-11T09:29:26Z

←Older revision		Revision as of 09:29, 11 August 2016
Line 1:		Line 1:
		+
	==A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2==		==A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2==
	<StructureSection load='474d' size='340' side='right' caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='474d' size='340' side='right' caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [http://www.ebi.ac.uk/pdbsum/474d 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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [http://pdbe.org/474d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [http://www.ebi.ac.uk/pdbsum/474d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=474d 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 474d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:34, 20 January 2015

2015-01-20T10:34:03Z

←Older revision		Revision as of 10:34, 20 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Chen, X.]]	+	[[Category: Chen, X]]
-	[[Category: Rao, S T.]]	+	[[Category: Rao, S T]]
-	[[Category: Sekar, K.]]	+	[[Category: Sekar, K]]
-	[[Category: Sundaralingam, M.]]	+	[[Category: Sundaralingam, M]]
	[[Category: B-dna/rna]]		[[Category: B-dna/rna]]
	[[Category: Complexed with drug]]		[[Category: Complexed with drug]]

OCA: Protected "474d" [edit=sysop:move=sysop]

2014-10-10T05:40:06Z

Protected "474d" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 10 October 2014

OCA at 05:40, 10 October 2014

2014-10-10T05:40:03Z

←Older revision		Revision as of 05:40, 10 October 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2==
-	[[~~Image:~~474d.~~png~~\|~~left~~\|~~200px~~]]	+	<StructureSection load='474d' size='340' side='right' caption='[[474d]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[474d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=474D FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</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=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=474d RCSB], [http://www.ebi.ac.uk/pdbsum/474d PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Netropsin is bound to the DNA decamer d(CCCCCIIIII)2, the C-4 bromo derivative d(CCCBr5CCIIIII)2and the C-2 bromo derivative d(CBr5CCCCIIIII)2in a novel 2:1 mode. Complexes of the native decamer and the C-4 bromo derivative are isomorphous, space group P1, unit cell dimensions a = 32.56 A (32.66), b = 32.59 A (32.77), c = 37.64 A (37.71), alpha = 86.30 degrees (86.01 degrees), beta = 84.50 degrees (84.37 degrees), gamma = 68.58 degrees (68.90 degrees) with two independent molecules (A and B) in the asymmetric unit (values in parentheses are for the derivative). The C-2 bromo derivative is hexagonal P61, unit cell dimensions a = b = 32.13 A, c = 143.92, gamma = 120 degrees with one molecule in the asymmetric unit. The structures were solved by the molecular replacement method. The novelty of the structures is that there are two netropsins bound end-to-end in the minor groove of each B-DNA decamer which has nearly a complete turn. The netropsins are held by hydrogen bonding interactions to the base atoms and by sandwiching van der Waal's interactions from the sugar-phosphate backbones of the double helix similar to every other drug.DNA complex. Each netropsin molecule spans approximately 5 bp. The netropsins refined with their guanidinium heads facing each other at the center, although an orientational disorder for the netropsins cannot be excluded. The amidinium ends stretch out toward the junctions and bind to the adjacent duplexes in the columns of stacked symmetry-related complexes. Both cationic ends of netropsin are bridged by water molecules in one of the independent molecules (molecule A) of the triclinic structures and also the hexagonal structure to form pseudo-continuous drug.decamer helices.

-	<!--	+	A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2.,Chen X, Mitra SN, Rao ST, Sekar K, Sundaralingam M Nucleic Acids Res. 1998 Dec 1;26(23):5464-71. PMID:9826773<ref>PMID:9826773</ref>
-	~~The line below this paragraph, containing "STRUCTURE_474d", creates~~ the ~~"Structure Box" on the page.~~	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter~~ (~~which sets the initial scene displayed when the page is loaded~~),	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_474d\| PDB=474d \| SCENE= }}~~	+

-	~~===A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_9826773}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 9826773 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_9826773}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA].~~	+
-		+
-	~~==Reference==~~	+
-	A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2., Chen X, Mitra SN, Rao ST, Sekar K, Sundaralingam M, Nucleic Acids Res. 1998 Dec 1;26(23):5464-71. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/9826773 9826773]~~	+
	[[Category: Chen, X.]]		[[Category: Chen, X.]]
	[[Category: Rao, S T.]]		[[Category: Rao, S T.]]
Line 30:		Line 25:
	[[Category: B-dna/rna]]		[[Category: B-dna/rna]]
	[[Category: Complexed with drug]]		[[Category: Complexed with drug]]
		+	[[Category: Dna]]
	[[Category: Double drug in minor groove]]		[[Category: Double drug in minor groove]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Mismatched]]		[[Category: Mismatched]]
	[[Category: Modified]]		[[Category: Modified]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:24:55 2008''

OCA at 10:24, 3 July 2008

2008-07-03T10:24:56Z

←Older revision		Revision as of 10:24, 3 July 2008
Line 1:		Line 1:
-	[[Image:474d.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:474d.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_474d\| PDB=474d \| SCENE= }}		{{STRUCTURE_474d\| PDB=474d \| SCENE= }}

-	~~'''~~A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2~~'''~~	+	===A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2===


-	~~==Overview==~~	+	<!--
-	~~Netropsin is bound to the DNA decamer d(CCCCCIIIII)2~~, the ~~C-4 bromo derivative d(CCCBr5CCIIIII)2and~~ the ~~C-2 bromo derivative d~~(~~CBr5CCCCIIIII)2in a novel 2~~:~~1 mode~~. ~~Complexes of the native decamer and the C-4 bromo derivative are isomorphous, space group P1, unit cell dimensions a = 32~~.~~56 A (32.66~~), b = 32.59 A (32.77), c = 37.64 A (37.71), alpha = 86.30 degrees (86.01 degrees), beta = 84.50 degrees (84.37 degrees), gamma = 68.58 degrees (68.90 degrees) with two independent molecules (A and B) in the asymmetric unit (values in parentheses are for the derivative). The C-2 bromo derivative is ~~hexagonal P61, unit cell dimensions a = b = 32.13 A, c = 143.92, gamma = 120 degrees with one molecule in~~ the ~~asymmetric unit~~. ~~The structures were solved by the molecular replacement method. The novelty of the structures is that there are two netropsins bound end~~-to-end in the minor groove of each B-DNA decamer which has nearly a complete turn. The netropsins are held by hydrogen bonding interactions to the base atoms and by sandwiching van der Waal's interactions from the sugar-phosphate backbones of the double helix similar to every other drug.DNA complex. Each netropsin molecule spans approximately 5 bp. The netropsins refined with their guanidinium heads facing each other at the center, although an orientational disorder for the netropsins cannot be excluded. The amidinium ends stretch out toward the junctions and bind to the adjacent duplexes in the columns of stacked symmetry-related complexes. Both cationic ends of netropsin are bridged by water molecules in one of the independent molecules (molecule A) of the triclinic structures and also the hexagonal structure to form pseudo-continuous drug.decamer helices.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9826773}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9826773 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9826773}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Mismatched]]		[[Category: Mismatched]]
	[[Category: Modified]]		[[Category: Modified]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:19:34 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:24:55 2008''

OCA at 19:19, 4 May 2008

2008-05-04T19:19:35Z

←Older revision		Revision as of 19:19, 4 May 2008
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	[[Image:474d.gif\|left\|200px]]		[[Image:474d.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 474d \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>474d</scene>~~, ~~resolution 2~~.~~400Å~~	+	The line below this paragraph, containing "STRUCTURE_474d", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=CBR:5~~-~~BROMO~~-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DI:2'-DEOXYINOSINE-5'-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=NT:NETROPSIN'>NT</scene>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_474d\| PDB=474d \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [http://www.ebi.ac.uk/pdbsum/474d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=474d RCSB]</span>	+
-	}}	+

	'''A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2'''		'''A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2'''
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	==About this Structure==		==About this Structure==
-	~~474D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA].	+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=474D OCA].

	==Reference==		==Reference==
	A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2., Chen X, Mitra SN, Rao ST, Sekar K, Sundaralingam M, Nucleic Acids Res. 1998 Dec 1;26(23):5464-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9826773 9826773]		A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2., Chen X, Mitra SN, Rao ST, Sekar K, Sundaralingam M, Nucleic Acids Res. 1998 Dec 1;26(23):5464-71. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9826773 9826773]
-	[[Category: Protein complex]]
	[[Category: Chen, X.]]		[[Category: Chen, X.]]
	[[Category: Rao, S T.]]		[[Category: Rao, S T.]]
	[[Category: Sekar, K.]]		[[Category: Sekar, K.]]
	[[Category: Sundaralingam, M.]]		[[Category: Sundaralingam, M.]]
-	[[Category: b-dna/rna]]	+	[[Category: B-dna/rna]]
-	[[Category: ~~complexed~~ with drug]]	+	[[Category: Complexed with drug]]
-	[[Category: ~~double~~ drug in minor groove]]	+	[[Category: Double drug in minor groove]]
-	[[Category: ~~double~~ helix]]	+	[[Category: Double helix]]
-	[[Category: ~~mismatched~~]]	+	[[Category: Mismatched]]
-	[[Category: ~~modified~~]]	+	[[Category: Modified]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:19:34 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:37:41 2008''	+

OCA at 02:37, 31 March 2008

2008-03-31T02:37:42Z

←Older revision		Revision as of 02:37, 31 March 2008
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	\|PDB= 474d \|SIZE=350\|CAPTION= <scene name='initialview01'>474d</scene>, resolution 2.400Å		\|PDB= 474d \|SIZE=350\|CAPTION= <scene name='initialview01'>474d</scene>, resolution 2.400Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=NT:NETROPSIN'>NT</scene>	+	\|LIGAND= <scene name='pdbligand=CBR:5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DI:2'-DEOXYINOSINE-5'-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=NT:NETROPSIN'>NT</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=474d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=474d OCA], [http://www.ebi.ac.uk/pdbsum/474d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=474d RCSB]</span>
	}}		}}

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	[[Category: Sekar, K.]]		[[Category: Sekar, K.]]
	[[Category: Sundaralingam, M.]]		[[Category: Sundaralingam, M.]]
-	[[Category: NT]]
	[[Category: b-dna/rna]]		[[Category: b-dna/rna]]
	[[Category: complexed with drug]]		[[Category: complexed with drug]]
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	[[Category: modified]]		[[Category: modified]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:08:41 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:41 2008''