6ode - Revision history

OCA at 07:08, 11 October 2023

2023-10-11T07:08:44Z

← Older revision		Revision as of 07:08, 11 October 2023
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	<StructureSection load='6ode' size='340' side='right'caption='[[6ode]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6ode' size='340' side='right'caption='[[6ode]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ode]] 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=6ODE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ODE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ode]] 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=6ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ODE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M9G:N-{(2S)-1-({(1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethyl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide'>M9G</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]] 2.9Å</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=M9G:N-{(2S)-1-({(1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethyl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide'>M9G</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=6ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ode OCA], [https://pdbe.org/6ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ode RCSB], [https://www.ebi.ac.uk/pdbsum/6ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ode 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=6ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ode OCA], [~~http~~://pdbe.org/6ode PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ode RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ode PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ode 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 ==
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	</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 11:58, 18 December 2019

2019-12-18T11:58:12Z

← Older revision		Revision as of 11:58, 18 December 2019
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	</div>		</div>
	<div class="pdbe-citations 6ode" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ode" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Proteasome 3D structures\|Proteasome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:01, 23 October 2019

2019-10-23T08:01:30Z

← Older revision		Revision as of 08:01, 23 October 2019
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	<StructureSection load='6ode' size='340' side='right'caption='[[6ode]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6ode' size='340' side='right'caption='[[6ode]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ode]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ODE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ODE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ode]] 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=6ODE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ODE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M9G:N-{(2S)-1-({(1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethyl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide'>M9G</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M9G:N-{(2S)-1-({(1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethyl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide'>M9G</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=6ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ode OCA], [http://pdbe.org/6ode PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ode RCSB], [http://www.ebi.ac.uk/pdbsum/6ode PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ode 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=6ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ode OCA], [http://pdbe.org/6ode PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ode RCSB], [http://www.ebi.ac.uk/pdbsum/6ode PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ode ProSAT]</span></td></tr>
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	</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

2019-10-10T05:21:32Z

@@ Line 1: / Line 1: @@
-The entry 6ode is ON HOLD  until Paper Publication
+==Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor B6==
-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 CEN208
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
 [[Category: Li, H]]
-[[Category: Hsu, H.C]]
+[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 04:07, 17 April 2019

2019-04-17T04:07:33Z

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

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

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

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

2019-04-03T04:44:03Z

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

← Older revision	Revision as of 04:44, 3 April 2019
(No difference)

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

2019-04-03T04:44:01Z

New page: '''Unreleased structure''' The entry 6ode 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 6ode is ON HOLD

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

Description: Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor CEN208
[[Category: Unreleased Structures]]
[[Category: Li, H]]
[[Category: Hsu, H.C]]