5qo7 - Revision history

OCA at 07:27, 17 October 2024

2024-10-17T07:27:20Z

← Older revision		Revision as of 07:27, 17 October 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DSBA_ECOLI DSBA_ECOLI] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.<ref>PMID:1429594</ref> <ref>PMID:22267510</ref>		[https://www.uniprot.org/uniprot/DSBA_ECOLI DSBA_ECOLI] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.<ref>PMID:1429594</ref> <ref>PMID:22267510</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein, we describe an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis. This approach yielded an 8-fold increase in affinity and detailed structural information for the resulting complex, providing an efficient and broadly applicable approach to early fragment development.

			Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX).,Bentley MR, Ilyichova OV, Wang G, Williams ML, Sharma G, Alwan WS, Whitehouse RL, Mohanty B, Scammells PJ, Heras B, Martin JL, Totsika M, Capuano B, Doak BC, Scanlon MJ J Med Chem. 2020 Jun 24. doi: 10.1021/acs.jmedchem.0c00111. PMID:32529824<ref>PMID:32529824</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5qo7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:08, 14 February 2024

2024-02-14T10:08:47Z

← Older revision		Revision as of 10:08, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='5qo7' size='340' side='right'caption='[[5qo7]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='5qo7' size='340' side='right'caption='[[5qo7]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5qo7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QO7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5QO7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5qo7]] 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=5QO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QO7 FirstGlance]. <br>
	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~dsbA (~~[~~http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax~~.~~cgi?mode=Info~~&~~srchmode=5&id=83333 ECOLI])~~</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]] 1.968Å</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=5qo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qo7 OCA], [~~http~~://pdbe.org/5qo7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5qo7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5qo7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5qo7 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=5qo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qo7 OCA], [https://pdbe.org/5qo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qo7 RCSB], [https://www.ebi.ac.uk/pdbsum/5qo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qo7 ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style~~=~~"background-color:#fffaf0;">~~		== Function ==
	=~~= Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/DSBA_ECOLI DSBA_ECOLI] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.<ref>PMID:1429594</ref> <ref>PMID:22267510</ref>
	~~A bottleneck~~ in ~~fragment-based lead development~~ is the ~~lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target~~. ~~Herein, we describe an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis~~. ~~This approach yielded an 8-fold increase in affinity and detailed structural information~~ for ~~the resulting complex, providing an efficient and broadly applicable approach to early fragment development~~.

	~~Rapid Elaboration of Fragments into Leads by X~~-~~ray Crystallographic Screening~~ of ~~Parallel Chemical Libraries (REFiLX~~).,Bentley MR, Ilyichova OV, Wang G, Williams ML, Sharma G, Alwan WS, Whitehouse RL, Mohanty B, Scammells PJ, Heras B, Martin JL, Totsika M, Capuano B, Doak BC, Scanlon MJ J Med Chem. 2020 Jun 24. doi: 10.1021/~~acs.jmedchem~~.~~0c00111. PMID:32529824~~<ref>PMID:~~32529824~~</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>
	~~</div>~~
	~~<div class="pdbe-citations 5qo7" style="background-color~~:~~#fffaf0;">~~</~~div~~>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bentley~~, M R~~]]		[[Category: Bentley MR]]
	[[Category: Doak~~, B C~~]]		[[Category: Doak BC]]
	[[Category: Ilyichova~~, O V~~]]		[[Category: Ilyichova OV]]
	[[Category: Scanlon~~, M J]]~~		[[Category: Scanlon MJ]]
	~~[[Category: Disulfide oxidoreductase]]~~
	~~[[Category: Dsba]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Redox protein~~]]

OCA at 14:22, 8 July 2020

2020-07-08T14:22:44Z

← Older revision		Revision as of 14:22, 8 July 2020
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	<StructureSection load='5qo7' size='340' side='right'caption='[[5qo7]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='5qo7' size='340' side='right'caption='[[5qo7]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5qo7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QO7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=5QO7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5qo7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QO7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5QO7 FirstGlance]. <br>
	</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=5qo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qo7 OCA], [http://pdbe.org/5qo7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qo7 RCSB], [http://www.ebi.ac.uk/pdbsum/5qo7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qo7 ProSAT]</span></td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5qo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qo7 OCA], [http://pdbe.org/5qo7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qo7 RCSB], [http://www.ebi.ac.uk/pdbsum/5qo7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qo7 ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein, we describe an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis. This approach yielded an 8-fold increase in affinity and detailed structural information for the resulting complex, providing an efficient and broadly applicable approach to early fragment development.

			Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX).,Bentley MR, Ilyichova OV, Wang G, Williams ML, Sharma G, Alwan WS, Whitehouse RL, Mohanty B, Scammells PJ, Heras B, Martin JL, Totsika M, Capuano B, Doak BC, Scanlon MJ J Med Chem. 2020 Jun 24. doi: 10.1021/acs.jmedchem.0c00111. PMID:32529824<ref>PMID:32529824</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5qo7" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bentley, M R]]		[[Category: Bentley, M R]]

OCA at 07:55, 5 February 2020

2020-02-05T07:55:47Z

← Older revision		Revision as of 07:55, 5 February 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry 5qo7 is ON HOLD until Paper Publication~~		==Group deposition of apo datasets for PANDDA analysis - Crystal Structure of apo EcDsbA after initial refinement (apo_dataset_37)==
			<StructureSection load='5qo7' size='340' side='right'caption='[[5qo7]], [[Resolution\|resolution]] 1.97Å' scene=''>
	~~Authors: Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J.~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[5qo7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QO7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5QO7 FirstGlance]. <br>
	~~Description:~~ Group deposition of apo datasets for PANDDA analysis -Crystal Structure of apo EcDsbA after initial refinement (apo_dataset_37)		</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=5qo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qo7 OCA], [http://pdbe.org/5qo7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qo7 RCSB], [http://www.ebi.ac.uk/pdbsum/5qo7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qo7 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Doak, B.C]]		__TOC__
	[[Category: Ilyichova, O.V]]		</StructureSection>
	[[Category: Scanlon, M.J]]		[[Category: Large Structures]]
	[[Category: ~~Bentley, M.R~~]]		[[Category: Bentley, M R]]
			[[Category: Doak, B C]]
			[[Category: Ilyichova, O V]]
			[[Category: Scanlon, M J]]
			[[Category: Disulfide oxidoreductase]]
			[[Category: Dsba]]
			[[Category: Oxidoreductase]]
			[[Category: Redox protein]]

OCA at 05:14, 10 April 2019

2019-04-10T05:14:45Z

← Older revision		Revision as of 05:14, 10 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5qo7 is ON HOLD		The entry 5qo7 is ON HOLD until Paper Publication

	Authors: Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J.		Authors: Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J.

OCA: Protected "5qo7" [edit=sysop:move=sysop]

2019-02-13T07:02:03Z

Protected "5qo7" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:02, 13 February 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5qo7 is ON HOLD Authors: Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J. Description: Group deposition of apo datasets for PANDDA analysi...

2019-02-13T07:02:01Z

New page: '''Unreleased structure''' The entry 5qo7 is ON HOLD Authors: Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J. Description: Group deposition of apo datasets for PANDDA analysi...

New page

'''Unreleased structure'''

The entry 5qo7 is ON HOLD

Authors: Ilyichova, O.V., Bentley, M.R., Doak, B.C., Scanlon, M.J.

Description: Group deposition of apo datasets for PANDDA analysis -Crystal Structure of apo EcDsbA after initial refinement (apo_dataset_37)
[[Category: Unreleased Structures]]
[[Category: Doak, B.C]]
[[Category: Ilyichova, O.V]]
[[Category: Scanlon, M.J]]
[[Category: Bentley, M.R]]