5tho - Revision history

OCA at 13:01, 4 October 2023

OCA — Wed, 04 Oct 2023 13:01:16 GMT

←Older revision		Revision as of 13:01, 4 October 2023
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	<StructureSection load='5tho' size='340' side='right'caption='[[5tho]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5tho' size='340' side='right'caption='[[5tho]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tho]] is a 28 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycta Mycta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5THO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5THO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tho]] is a 28 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5THO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5THO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=7C7:N~~,~~N-DIETHYL-N~2~-(3-PHENYLPROPANOYL)-L-ASPARAGINYL-O-METHYL-N-~~[~~(NAPHTHALEN-1-YL)METHYL~~]~~-L-SERINAMIDE'>7C7</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]] 3.002Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>prcA, MRA_2124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=419947 MYCTA]), prcB, MRA_2125 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7C7:N,N-DIETHYL-N~2~-(3-PHENYLPROPANOYL)-L-ASPARAGINYL-O-METHYL-N-[(NAPHTHALEN-1-YL)METHYL]-L-SERINAMIDE'>7C7</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=5tho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tho OCA], [https://pdbe.org/5tho PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tho RCSB], [https://www.ebi.ac.uk/pdbsum/5tho PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tho 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=5tho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tho OCA], [~~http~~://pdbe.org/5tho PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tho RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tho PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tho ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PSA_MYCTA PSA_MYCTA~~]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. [[http://www.uniprot.org/uniprot/PSB_MYCTA PSB_MYCTA]~~] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.	+	[https://www.uniprot.org/uniprot/PSA_MYCTA PSA_MYCTA] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.
	<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: ~~Mycta]]~~	+	[[Category: Mycobacterium tuberculosis H37Ra]]
-	~~[[Category: Proteasome endopeptidase complex~~]]	+	[[Category: Hsu HC]]
-	[[Category: Hsu~~, H C~~]]	+	[[Category: Li H]]
-	[[Category: Li, H]]	+
-	~~[[Category: Dipeptide inhibitor]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Mycobacterium tuberculosis]]~~	+
-	~~[[Category: Proteasome~~]]	+

OCA at 09:52, 12 August 2020

OCA — Wed, 12 Aug 2020 09:52:35 GMT

←Older revision		Revision as of 09:52, 12 August 2020
Line 1:		Line 1:

	==Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped Dipeptide Inhibitor PKS2205==		==Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped Dipeptide Inhibitor PKS2205==
-	<StructureSection load='5tho' size='340' side='right' caption='[[5tho]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5tho' size='340' side='right'caption='[[5tho]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tho]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5THO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5THO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tho]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5THO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5THO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7C7:N,N-DIETHYL-N~2~-(3-PHENYLPROPANOYL)-L-ASPARAGINYL-O-METHYL-N-[(NAPHTHALEN-1-YL)METHYL]-L-SERINAMIDE'>7C7</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7C7:N,N-DIETHYL-N~2~-(3-PHENYLPROPANOYL)-L-ASPARAGINYL-O-METHYL-N-[(NAPHTHALEN-1-YL)METHYL]-L-SERINAMIDE'>7C7</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">prcA, MRA_2124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA]), prcB, MRA_2125 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</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=5tho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tho OCA], [http://pdbe.org/5tho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tho RCSB], [http://www.ebi.ac.uk/pdbsum/5tho PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tho 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=5tho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tho OCA], [http://pdbe.org/5tho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tho RCSB], [http://www.ebi.ac.uk/pdbsum/5tho PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tho ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5tho" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5tho" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycta]]
	[[Category: Proteasome endopeptidase complex]]		[[Category: Proteasome endopeptidase complex]]
	[[Category: Hsu, H C]]		[[Category: Hsu, H C]]

OCA at 07:32, 18 January 2017

OCA — Wed, 18 Jan 2017 07:32:17 GMT

←Older revision		Revision as of 07:32, 18 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tho is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped Dipeptide Inhibitor PKS2205==
		+	<StructureSection load='5tho' size='340' side='right' caption='[[5tho]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tho]] is a 28 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5THO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5THO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7C7:N,N-DIETHYL-N~2~-(3-PHENYLPROPANOYL)-L-ASPARAGINYL-O-METHYL-N-[(NAPHTHALEN-1-YL)METHYL]-L-SERINAMIDE'>7C7</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=5tho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tho OCA], [http://pdbe.org/5tho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tho RCSB], [http://www.ebi.ac.uk/pdbsum/5tho PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tho ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PSA_MYCTA PSA_MYCTA]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. [[http://www.uniprot.org/uniprot/PSB_MYCTA PSB_MYCTA]] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Mycobacterium tuberculosis (Mtb) 20S proteasome is vital for the pathogen to survive under nitrosative stress in vitro and to persist in mice. To qualify for drug development, inhibitors targeting Mtb 20S must spare both the human constitutive proteasome (c-20S) and immunoproteasome (i-20S). We recently reported members of a family of noncovalently binding dipeptide proteasome inhibitors that are highly potent and selective for Mtb 20S over human c-20S and i-20S. To understand the structural basis of their potency and selectivity, we have studied the structure-activity relationship of six derivatives and solved their cocrystal structures with Mtb 20S. The dipeptide inhibitors form an antiparallel beta-strand with the active site beta-strands. Selectivity is conferred by several features of Mtb 20S relative to its mouse counterparts, including a larger S1 pocket, additional hydrogen bonds in the S3 pocket, and hydrophobic interactions in the S4 pocket. Serine-20 and glutamine-22 of Mtb 20S interact with the dipeptides and confer Mtb-specific inhibition over c-20S and i-20S. The Mtb 20S and mammalian i-20S have a serine-27 that interacts strongly with the dipeptides, potentially explaining the higher inhibitory activity of the dipeptides toward i-20S over c-20S. This detailed structural knowledge will aid in optimizing the dipeptides as anti-tuberculosis drugs.

-	~~Authors:~~ Hsu, H.-C., ~~Huilin, L~~.	+	Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome.,Hsu HC, Singh PK, Fan H, Wang R, Sukenick G, Nathan C, Lin G, Li H Biochemistry. 2017 Jan 10;56(1):324-333. doi: 10.1021/acs.biochem.6b01107. Epub, 2016 Dec 27. PMID:27976853<ref>PMID:27976853</ref>

-	~~Description: Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N~~,C-~~capped Dipeptide Inhibitor PKS2205~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Huilin~~, L]]	+	<div class="pdbe-citations 5tho" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Hsu~~, H.-C]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Proteasome endopeptidase complex]]
		+	[[Category: Hsu, H C]]
		+	[[Category: Li, H]]
		+	[[Category: Dipeptide inhibitor]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Proteasome]]

OCA at 17:04, 26 October 2016

OCA — Wed, 26 Oct 2016 17:04:33 GMT

←Older revision		Revision as of 17:04, 26 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tho is ON HOLD	+	The entry 5tho is ON HOLD until Paper Publication

	Authors: Hsu, H.-C., Huilin, L.		Authors: Hsu, H.-C., Huilin, L.

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

OCA — Wed, 19 Oct 2016 15:49:28 GMT

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

←Older revision

Revision as of 15:49, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tho is ON HOLD Authors: Hsu, H.-C., Huilin, L. Description: Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped ...

OCA — Wed, 19 Oct 2016 15:49:26 GMT

New page: '''Unreleased structure''' The entry 5tho is ON HOLD Authors: Hsu, H.-C., Huilin, L. Description: Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped ...

New page

'''Unreleased structure'''

The entry 5tho is ON HOLD

Authors: Hsu, H.-C., Huilin, L.

Description: Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped Dipeptide Inhibitor PKS2205
[[Category: Unreleased Structures]]
[[Category: Huilin, L]]
[[Category: Hsu, H.-C]]