6cn8 - Revision history

OCA at 15:07, 4 October 2023

2023-10-04T15:07:50Z

←Older revision		Revision as of 15:07, 4 October 2023
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	<StructureSection load='6cn8' size='340' side='right'caption='[[6cn8]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6cn8' size='340' side='right'caption='[[6cn8]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cn8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~] and [~~http~~://en.wikipedia.org/wiki/Streptomyces_atratus Streptomyces atratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CN8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CN8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cn8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] and [https://en.wikipedia.org/wiki/Streptomyces_atratus Streptomyces atratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CN8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=F7P:'>F7P</scene>, <scene name='pdbligand=F7S:'>F7S</scene>, <scene name='pdbligand=F7V:'>F7V</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F7P:1-[(3R)-3-hydroxy-2-methylbutan-2-yl]-L-tryptophan'>F7P</scene>, <scene name='pdbligand=F7S:(4S)-5-hydroxy-N-methyl-L-leucine'>F7S</scene>, <scene name='pdbligand=F7V:(2S,4E)-2-aminohex-4-enoic+acid'>F7V</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">clpC1, Rv3596c, MTCY07H7B.26 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])~~</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=6cn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cn8 OCA], [https://pdbe.org/6cn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cn8 RCSB], [https://www.ebi.ac.uk/pdbsum/6cn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cn8 ProSAT]</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=6cn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cn8 OCA], [~~http~~://pdbe.org/6cn8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cn8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cn8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cn8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CLPC1_MYCTU CLPC1_MYCTU]] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP (By similarity). Degrades anti-sigma-E factor RseA in the presence of ClpP2.	+	[https://www.uniprot.org/uniprot/CLPC1_MYCTU CLPC1_MYCTU] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP (By similarity). Degrades anti-sigma-E factor RseA in the presence of ClpP2.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6cn8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cn8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Clp protease 3D structures\|Clp protease 3D structures]]
		+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Streptomyces atratus]]
-	[[Category: Abad-Zapatero, C]]
-	[[Category: Wolf, N W]]
-	[[Category: Atp-dependent protease]]
-	[[Category: Atpase aaa+]]
-	[[Category: Chaperone]]
-	[[Category: Chaperone-antibiotic complex]]
-	[[Category: Clpc1-ntd]]
-	[[Category: Macrocyclic peptide]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Natural product~~]]	+	[[Category: Streptomyces atratus]]
-	[[Category: ~~Rufomycin i~~]]	+	[[Category: Abad-Zapatero C]]
		+	[[Category: Wolf NW]]

OCA at 07:20, 26 June 2019

2019-06-26T07:20:40Z

←Older revision		Revision as of 07:20, 26 June 2019
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	<StructureSection load='6cn8' size='340' side='right'caption='[[6cn8]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6cn8' size='340' side='right'caption='[[6cn8]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cn8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Streptomyces_atratus Streptomyces atratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CN8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cn8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884] and [http://en.wikipedia.org/wiki/Streptomyces_atratus Streptomyces atratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CN8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F7P:'>F7P</scene>, <scene name='pdbligand=F7S:'>F7S</scene>, <scene name='pdbligand=F7V:'>F7V</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F7P:'>F7P</scene>, <scene name='pdbligand=F7S:'>F7S</scene>, <scene name='pdbligand=F7V:'>F7V</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpC1, Rv3596c, MTCY07H7B.26 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6cn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cn8 OCA], [http://pdbe.org/6cn8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cn8 RCSB], [http://www.ebi.ac.uk/pdbsum/6cn8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cn8 ProSAT]</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=6cn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cn8 OCA], [http://pdbe.org/6cn8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cn8 RCSB], [http://www.ebi.ac.uk/pdbsum/6cn8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cn8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 22:41, 5 June 2019

2019-06-05T22:41:25Z

←Older revision		Revision as of 22:41, 5 June 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6cn8 is ~~ON HOLD~~	+	==High-resolution structure of ClpC1-NTD binding to Rufomycin-I==
		+	<StructureSection load='6cn8' size='340' side='right'caption='[[6cn8]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cn8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Streptomyces_atratus Streptomyces atratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CN8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F7P:'>F7P</scene>, <scene name='pdbligand=F7S:'>F7S</scene>, <scene name='pdbligand=F7V:'>F7V</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</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=6cn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cn8 OCA], [http://pdbe.org/6cn8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cn8 RCSB], [http://www.ebi.ac.uk/pdbsum/6cn8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cn8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CLPC1_MYCTU CLPC1_MYCTU]] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP (By similarity). Degrades anti-sigma-E factor RseA in the presence of ClpP2.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis ( M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. The outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.

-	~~Authors~~:	+	High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads.,Wolf NM, Lee H, Choules MP, Pauli GF, Phansalkar R, Anderson JR, Gao W, Ren J, Santarsiero BD, Lee H, Cheng J, Jin YY, Ho NA, Duc NM, Suh JW, Abad-Zapatero C, Cho S ACS Infect Dis. 2019 May 3. doi: 10.1021/acsinfecdis.8b00276. PMID:30990022<ref>PMID:30990022</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6cn8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptomyces atratus]]
		+	[[Category: Abad-Zapatero, C]]
		+	[[Category: Wolf, N W]]
		+	[[Category: Atp-dependent protease]]
		+	[[Category: Atpase aaa+]]
		+	[[Category: Chaperone]]
		+	[[Category: Chaperone-antibiotic complex]]
		+	[[Category: Clpc1-ntd]]
		+	[[Category: Macrocyclic peptide]]
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Natural product]]
		+	[[Category: Rufomycin i]]

OCA at 04:11, 29 May 2019

2019-05-29T04:11:40Z

←Older revision		Revision as of 04:11, 29 May 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cn8 is ON HOLD ~~until Paper Publication~~	+	The entry 6cn8 is ON HOLD

	Authors:		Authors:

OCA at 03:58, 30 May 2018

2018-05-30T03:58:32Z

←Older revision		Revision as of 03:58, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cn8 is ON HOLD	+	The entry 6cn8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6cn8" [edit=sysop:move=sysop]

2018-03-14T05:12:17Z

Protected "6cn8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:12, 14 March 2018

OCA: New page: '''Unreleased structure''' The entry 6cn8 is ON HOLD Authors: Description: Category: Unreleased Structures

2018-03-14T05:12:16Z

New page: '''Unreleased structure''' The entry 6cn8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6cn8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]