6wck - Revision history

OCA at 14:21, 18 October 2023

OCA — Wed, 18 Oct 2023 14:21:46 GMT

←Older revision		Revision as of 14:21, 18 October 2023
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	<StructureSection load='6wck' size='340' side='right'caption='[[6wck]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6wck' size='340' side='right'caption='[[6wck]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6wck]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WCK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WCK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wck]] 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=6WCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WCK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.801Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[6n65\|6n65]]~~</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=6wck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wck OCA], [https://pdbe.org/6wck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wck RCSB], [https://www.ebi.ac.uk/pdbsum/6wck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wck 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=6wck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wck OCA], [~~http~~://pdbe.org/6wck PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wck RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wck PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wck 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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bond~~, C S~~]]	+	[[Category: Bond CS]]
-	[[Category: Iyer~~, K S~~]]	+	[[Category: Iyer KS]]
-	[[Category: Ou, A]]	+	[[Category: Ou A]]
-	[[Category: Schmidberger~~, J W~~]]	+	[[Category: Schmidberger JW]]
-	[[Category: Smith~~, N M]]~~	+	[[Category: Smith NM]]
-	~~[[Category: Bromouracil]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: G-quadruplex]]~~	+
-	~~[[Category: G16t mutant]]~~	+
-	~~[[Category: Kra]]~~	+
-	~~[[Category: Promoter sequence~~]]	+

OCA at 06:44, 6 May 2020

OCA — Wed, 06 May 2020 06:44:47 GMT

←Older revision		Revision as of 06:44, 6 May 2020
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	==KRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16.==		==KRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16.==
-	<StructureSection load='6wck' size='340' side='right'caption='[[6wck]]' scene=''>	+	<StructureSection load='6wck' size='340' side='right'caption='[[6wck]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WCK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WCK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wck]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WCK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WCK FirstGlance]. <br>
-	</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=6wck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wck OCA], [http://pdbe.org/6wck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wck RCSB], [http://www.ebi.ac.uk/pdbsum/6wck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wck ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n65\|6n65]]</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=6wck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wck OCA], [http://pdbe.org/6wck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wck RCSB], [http://www.ebi.ac.uk/pdbsum/6wck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wck ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 A) of a KRAS G-quadruplex as a 5'-head-to-head dimer with extensive poly-A pi-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A pi-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5'-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.
		+
		+	High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A pi-stacking interactions for small-molecule recognition.,Ou A, Schmidberger JW, Wilson KA, W Evans C, Hargreaves JA, Grigg M, O'Mara ML, Iyer KS, Bond CS, Smith NM Nucleic Acids Res. 2020 Apr 20. pii: 5822969. doi: 10.1093/nar/gkaa262. PMID:32313953<ref>PMID:32313953</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wck" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bond CS]]	+	[[Category: Bond, C S]]
-	[[Category: Iyer KS]]	+	[[Category: Iyer, K S]]
-	[[Category: Ou A]]	+	[[Category: Ou, A]]
-	[[Category: Schmidberger JW]]	+	[[Category: Schmidberger, J W]]
-	[[Category: Smith NM]]	+	[[Category: Smith, N M]]
		+	[[Category: Bromouracil]]
		+	[[Category: Dna]]
		+	[[Category: G-quadruplex]]
		+	[[Category: G16t mutant]]
		+	[[Category: Kra]]
		+	[[Category: Promoter sequence]]

OCA at 07:04, 15 April 2020

OCA — Wed, 15 Apr 2020 07:04:36 GMT

←Older revision		Revision as of 07:04, 15 April 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6wck is ~~ON HOLD~~	+	==KRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16.==
-		+	<StructureSection load='6wck' size='340' side='right'caption='[[6wck]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WCK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WCK FirstGlance]. <br>
-	~~Description~~:	+	</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=6wck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wck OCA], [http://pdbe.org/6wck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wck RCSB], [http://www.ebi.ac.uk/pdbsum/6wck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wck ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bond CS]]
		+	[[Category: Iyer KS]]
		+	[[Category: Ou A]]
		+	[[Category: Schmidberger JW]]
		+	[[Category: Smith NM]]

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

OCA — Wed, 08 Apr 2020 05:36:46 GMT

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

←Older revision

Revision as of 05:36, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 6wck is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Apr 2020 05:36:45 GMT

New page: '''Unreleased structure''' The entry 6wck is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6wck is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]