6pg2 - Revision history

OCA at 12:59, 6 November 2024

2024-11-06T12:59:19Z

← Older revision		Revision as of 12:59, 6 November 2024
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	<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[6pg2]] 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=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PG2 FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PG2 FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.91Å</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]] 1.91Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=O6Y:2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile'>O6Y</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=O6Y:2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile'>O6Y</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=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [https://pdbe.org/6pg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [https://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 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=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [https://pdbe.org/6pg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [https://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 ProSAT]</span></td></tr>
	</table>		</table>
	~~== 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>
	~~<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 6pg2" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Escherichia coli K-12]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bentley M]]		[[Category: Bentley M]]

OCA at 07:28, 11 October 2023

2023-10-11T07:28:44Z

← Older revision		Revision as of 07:28, 11 October 2023
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	<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6pg2]] 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=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PG2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pg2]] 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=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PG2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=O6Y:2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile'>O6Y</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]] 1.91Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pbi\|6pbi]]</td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=O6Y:2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile'>O6Y</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbA, dsf, ppfA, b3860, JW3832 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [https://pdbe.org/6pg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [https://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 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=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [~~http~~://pdbe.org/6pg2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bentley, M]]		[[Category: Bentley M]]
	[[Category: Doak, B]]		[[Category: Doak B]]
	[[Category: Ilyichova~~, O V~~]]		[[Category: Ilyichova OV]]
	[[Category: Scanlon~~, M J]]~~		[[Category: Scanlon MJ]]
	~~[[Category: Disulfide oxidoreductase]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Oxidoreductase-inhibitor complex]]~~
	~~[[Category: Redox protein]]~~
	~~[[Category: Refilx~~]]

OCA at 08:08, 11 November 2020

2020-11-11T08:08:00Z

← Older revision		Revision as of 08:08, 11 November 2020
Line 1:		Line 1:

	==Crystal Structure of EcDsbA in a complex with unpurified reaction product H5 (morpholine 8)==		==Crystal Structure of EcDsbA in a complex with unpurified reaction product H5 (morpholine 8)==
	<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]]' scene=''>		<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]], [[Resolution\|resolution]] 1.91Å' 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=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PG2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pg2]] 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=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PG2 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=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [http://pdbe.org/6pg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [http://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=O6Y:2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile'>O6Y</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pbi\|6pbi]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbA, dsf, ppfA, b3860, JW3832 ([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=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [http://pdbe.org/6pg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [http://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://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 6pg2" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bentley M]]		[[Category: Bentley, M]]
	[[Category: Doak B]]		[[Category: Doak, B]]
	[[Category: Ilyichova OV]]		[[Category: Ilyichova, O V]]
	[[Category: Scanlon MJ]]		[[Category: Scanlon, M J]]
			[[Category: Disulfide oxidoreductase]]
			[[Category: Oxidoreductase]]
			[[Category: Oxidoreductase-inhibitor complex]]
			[[Category: Redox protein]]
			[[Category: Refilx]]

OCA at 06:01, 6 May 2020

2020-05-06T06:01:27Z

← Older revision		Revision as of 06:01, 6 May 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6pg2 is ~~ON HOLD until Paper Publication~~		==Crystal Structure of EcDsbA in a complex with unpurified reaction product H5 (morpholine 8)==
			<StructureSection load='6pg2' size='340' side='right'caption='[[6pg2]]' scene=''>
	~~Authors~~: ~~Ilyichova~~, O.V., ~~Bentley~~, M., ~~Doak, B~~., ~~Scanlon, M~~.J.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PG2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PG2 FirstGlance]. <br>
	~~Description: Crystal Structure of EcDsbA in a complex with unpurified reaction product H5 (Compound 5)~~		</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=6pg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pg2 OCA], [http://pdbe.org/6pg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pg2 RCSB], [http://www.ebi.ac.uk/pdbsum/6pg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pg2 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Bentley, M]]		__TOC__
	[[Category: ~~Ilyichova, O.V~~]]		</StructureSection>
	[[Category: ~~Scanlon, M.J~~]]		[[Category: Large Structures]]
	[[Category: ~~Doak, B~~]]		[[Category: Bentley M]]
			[[Category: Doak B]]
			[[Category: Ilyichova OV]]
			[[Category: Scanlon MJ]]

OCA at 04:06, 10 July 2019

2019-07-10T04:06:32Z

← Older revision		Revision as of 04:06, 10 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6pg2 is ON HOLD		The entry 6pg2 is ON HOLD until Paper Publication

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

OCA: Protected "6pg2" [edit=sysop:move=sysop]

2019-07-03T04:17:15Z

Protected "6pg2" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:17, 3 July 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6pg2 is ON HOLD Authors: Ilyichova, O.V., Bentley, M., Doak, B., Scanlon, M.J. Description: Crystal Structure of EcDsbA in a complex with unpurifie...

2019-07-03T04:17:13Z

New page: '''Unreleased structure''' The entry 6pg2 is ON HOLD Authors: Ilyichova, O.V., Bentley, M., Doak, B., Scanlon, M.J. Description: Crystal Structure of EcDsbA in a complex with unpurifie...

New page

'''Unreleased structure'''

The entry 6pg2 is ON HOLD

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

Description: Crystal Structure of EcDsbA in a complex with unpurified reaction product H5 (Compound 5)
[[Category: Unreleased Structures]]
[[Category: Bentley, M]]
[[Category: Ilyichova, O.V]]
[[Category: Scanlon, M.J]]
[[Category: Doak, B]]