6ocw - Revision history

OCA at 07:08, 11 October 2023

OCA — Wed, 11 Oct 2023 07:08:19 GMT

←Older revision		Revision as of 07:08, 11 October 2023
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	<StructureSection load='6ocw' size='340' side='right'caption='[[6ocw]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6ocw' size='340' side='right'caption='[[6ocw]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ocw]] is a 28 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OCW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ocw]] is a 28 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OCW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=M6M:N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide+(non-preferred+name)'>M6M</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]] 2.6Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">prcA, Rv2109c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=M6M:N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide+(non-preferred+name)'>M6M</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=6ocw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ocw OCA], [https://pdbe.org/6ocw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ocw RCSB], [https://www.ebi.ac.uk/pdbsum/6ocw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ocw 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=6ocw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ocw OCA], [~~http~~://pdbe.org/6ocw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ocw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ocw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ocw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PSA_MYCTU PSA_MYCTU]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref> [[http://www.uniprot.org/uniprot/PSB_MYCTU PSB_MYCTU]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref>	+	[https://www.uniprot.org/uniprot/PSA_MYCTU PSA_MYCTU] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu]]~~	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	~~[[Category: Proteasome endopeptidase complex~~]]	+	[[Category: Hsu HC]]
-	[[Category: Hsu~~, H C~~]]	+	[[Category: Li H]]
-	[[Category: Li, H]]	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Mycobacterium tuberculosis]]~~	+
-	~~[[Category: Phenylimidazole]]~~	+
-	~~[[Category: Proteasome inhibitor~~]]	+

OCA at 11:57, 18 December 2019

OCA — Wed, 18 Dec 2019 11:57:55 GMT

←Older revision		Revision as of 11:57, 18 December 2019
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6ocw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ocw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:01, 23 October 2019

OCA — Wed, 23 Oct 2019 08:01:11 GMT

←Older revision		Revision as of 08:01, 23 October 2019
Line 3:		Line 3:
	<StructureSection load='6ocw' size='340' side='right'caption='[[6ocw]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6ocw' size='340' side='right'caption='[[6ocw]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ocw]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OCW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ocw]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OCW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=M6M:N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide+(non-preferred+name)'>M6M</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=M6M:N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide+(non-preferred+name)'>M6M</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">prcA, Rv2109c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), prcB, Rv2110c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=6ocw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ocw OCA], [http://pdbe.org/6ocw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ocw RCSB], [http://www.ebi.ac.uk/pdbsum/6ocw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ocw 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=6ocw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ocw OCA], [http://pdbe.org/6ocw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ocw RCSB], [http://www.ebi.ac.uk/pdbsum/6ocw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ocw ProSAT]</span></td></tr>
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]
	[[Category: Hsu, H C]]		[[Category: Hsu, H C]]

OCA at 05:21, 10 October 2019

OCA — Thu, 10 Oct 2019 05:21:29 GMT

←Older revision		Revision as of 05:21, 10 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ocw is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor A85==
		+	<StructureSection load='6ocw' size='340' side='right'caption='[[6ocw]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ocw]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OCW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=M6M:N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide+(non-preferred+name)'>M6M</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=6ocw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ocw OCA], [http://pdbe.org/6ocw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ocw RCSB], [http://www.ebi.ac.uk/pdbsum/6ocw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ocw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PSA_MYCTU PSA_MYCTU]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref> [[http://www.uniprot.org/uniprot/PSB_MYCTU PSB_MYCTU]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The M.tuberculosis proteasome is able to cleave oligopeptides not only after hydrophobic but also after basic, acidic and small neutral residues. Among the identified substrates of the M.tuberculosis proteasome are the pupylated FabD, PanB and Mpa proteins. One function of the proteasome is to contribute to M.tuberculosis ability to resist killing by host macrophages, since the core proteasome is essential for persistence of the pathogen during the chronic phase of infection in mice. The mechanism of protection against bactericidal chemistries of the host's immune response probably involves the degradation of proteins that are irreversibly oxidized, nitrated, or nitrosated.<ref>PMID:16468985</ref> <ref>PMID:18059281</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Co-evolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders non-replicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial rather than human proteasomes.

-	~~Authors:~~ Hsu, ~~H.C.~~, Li, H.	+	Selective Phenylimidazole-based Inhibitors of the Mycobacterium tuberculosis Proteasome.,Zhan W, Hsu HC, Morgan T, Ouellette T, Burns-Huang K, Hara R, Wright AG, Imaeda T, Okamoto R, Sato K, Michino M, Ramjee M, Aso K, Meinke P, Foley M, Nathan CF, Li H, Lin G J Med Chem. 2019 Sep 27. doi: 10.1021/acs.jmedchem.9b01187. PMID:31560200<ref>PMID:31560200</ref>

-	~~Description: Crystal Structure~~ of ~~Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole~~-~~based Inhibitor CEN168~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ocw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Proteasome endopeptidase complex]]
		+	[[Category: Hsu, H C]]
	[[Category: Li, H]]		[[Category: Li, H]]
-	[[Category: ~~Hsu, H.C~~]]	+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Phenylimidazole]]
		+	[[Category: Proteasome inhibitor]]

OCA at 04:07, 17 April 2019

OCA — Wed, 17 Apr 2019 04:07:16 GMT

←Older revision		Revision as of 04:07, 17 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Hsu, H.C., Li, H.		Authors: Hsu, H.C., Li, H.

-	Description: Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor ~~CEN16~~	+	Description: Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor CEN168
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Li, H]]		[[Category: Li, H]]
	[[Category: Hsu, H.C]]		[[Category: Hsu, H.C]]

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

OCA — Wed, 03 Apr 2019 04:41:14 GMT

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

←Older revision

Revision as of 04:41, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6ocw is ON HOLD Authors: Hsu, H.C., Li, H. Description: Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-...

OCA — Wed, 03 Apr 2019 04:41:12 GMT

New page: '''Unreleased structure''' The entry 6ocw is ON HOLD Authors: Hsu, H.C., Li, H. Description: Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-...

New page

'''Unreleased structure'''

The entry 6ocw is ON HOLD

Authors: Hsu, H.C., Li, H.

Description: Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor CEN16
[[Category: Unreleased Structures]]
[[Category: Li, H]]
[[Category: Hsu, H.C]]