7dor - Revision history

OCA at 16:37, 29 November 2023

OCA — Wed, 29 Nov 2023 16:37:14 GMT

←Older revision		Revision as of 16:37, 29 November 2023
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	==E. coli GyrB ATPase domain in complex with 4-nitropheno==		==E. coli GyrB ATPase domain in complex with 4-nitropheno==
-	<StructureSection load='7dor' size='340' side='right'caption='[[7dor]]' scene=''>	+	<StructureSection load='7dor' size='340' side='right'caption='[[7dor]], [[Resolution\|resolution]] 1.89Å' 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=7DOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DOR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dor]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DOR FirstGlance]. <br>
-	</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=7dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dor OCA], [https://pdbe.org/7dor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dor RCSB], [https://www.ebi.ac.uk/pdbsum/7dor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dor ProSAT]</span></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]] 1.89Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AX7:1H-BENZIMIDAZOL-2-AMINE'>AX7</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=7dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dor OCA], [https://pdbe.org/7dor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dor RCSB], [https://www.ebi.ac.uk/pdbsum/7dor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dor ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GYRB_ECOLI GYRB_ECOLI] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.<ref>PMID:12051843</ref> <ref>PMID:18642932</ref> <ref>PMID:20675723</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA gyrase is an essential DNA topoisomerase that exists only in bacteria. Since novobiocin was withdrawn from the market, new scaffolds and new mechanistic GyrB inhibitors are urgently needed. In this study, we employed fragment screening and X-ray crystallography to identify new building blocks, as well as their binding mechanisms, to support the discovery of new GyrB inhibitors. In total, 84 of the 618 chemical fragments were shown to either thermally stabilize the ATPase domain of Escherichia coli GyrB or inhibit the ATPase activity of E. coli gyrase. Among them, the IC50 values of fragments 10 and 23 were determined to be 605.3 muM and 446.2 muM, respectively. Cocrystal structures of the GyrB ATPase domain with twelve fragment hits were successfully determined at a high resolution. All twelve fragments were deeply inserted in the pocket and formed H-bonds with Asp73 and Thr165, and six fragments formed an additional H-bond with the backbone oxygen of Val71. Fragment screening further highlighted the capability of Asp73, Thr165 and Val71 to bind chemicals and provided diverse building blocks for the design of GyrB inhibitors.
		+
		+	Identification of new building blocks by fragment screening for discovering GyrB inhibitors.,Yu Y, Guo J, Cai Z, Ju Y, Xu J, Gu Q, Zhou H Bioorg Chem. 2021 Sep;114:105040. doi: 10.1016/j.bioorg.2021.105040. Epub 2021, May 31. PMID:34098257<ref>PMID:34098257</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dor" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Yu Y]]		[[Category: Yu Y]]
	[[Category: Zhou H]]		[[Category: Zhou H]]

OCA at 14:09, 27 October 2021

OCA — Wed, 27 Oct 2021 14:09:57 GMT

←Older revision		Revision as of 14:09, 27 October 2021
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-	'''Unreleased structure'''

-	~~The entry 7dor is ON HOLD until Paper Publication~~	+	==E. coli GyrB ATPase domain in complex with 4-nitropheno==
-		+	<StructureSection load='7dor' size='340' side='right'caption='[[7dor]]' scene=''>
-	~~Authors: Yu, Y., Zhou, H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DOR FirstGlance]. <br>
-	~~Description:~~ E. coli GyrB ATPase domain in complex with 4-nitropheno	+	</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=7dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dor OCA], [https://pdbe.org/7dor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dor RCSB], [https://www.ebi.ac.uk/pdbsum/7dor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dor ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Zhou~~, H]]	+	__TOC__
-	[[Category: Yu, Y]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Yu Y]]
		+	[[Category: Zhou H]]

OCA at 05:21, 30 December 2020

OCA — Wed, 30 Dec 2020 05:21:28 GMT

←Older revision		Revision as of 05:21, 30 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dor is ON HOLD	+	The entry 7dor is ON HOLD until Paper Publication

	Authors: Yu, Y., Zhou, H.		Authors: Yu, Y., Zhou, H.

OCA: Protected "7dor" [edit=sysop:move=sysop]

OCA — Thu, 24 Dec 2020 07:56:16 GMT

Protected "7dor" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:56, 24 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dor is ON HOLD Authors: Yu, Y., Zhou, H. Description: E. coli GyrB ATPase domain in complex with 4-nitropheno Category: Unreleased Structures ...

OCA — Thu, 24 Dec 2020 07:56:14 GMT

New page: '''Unreleased structure''' The entry 7dor is ON HOLD Authors: Yu, Y., Zhou, H. Description: E. coli GyrB ATPase domain in complex with 4-nitropheno Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 7dor is ON HOLD

Authors: Yu, Y., Zhou, H.

Description: E. coli GyrB ATPase domain in complex with 4-nitropheno
[[Category: Unreleased Structures]]
[[Category: Zhou, H]]
[[Category: Yu, Y]]