6c6o - Revision history

OCA at 14:57, 4 October 2023

OCA — Wed, 04 Oct 2023 14:57:14 GMT

←Older revision		Revision as of 14:57, 4 October 2023
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	<StructureSection load='6c6o' size='340' side='right'caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6c6o' size='340' side='right'caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C6O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C6O FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ENG:(2Z)~~-~~4-(~~2~~-bromo-4-hydroxyphenyl)-2-hydroxy-4-oxobut-2-enoic+acid'>ENG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>glcB ([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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ENG:(2Z)-4-(2-bromo-4-hydroxyphenyl)-2-hydroxy-4-oxobut-2-enoic+acid'>ENG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Malate_synthase Malate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.3.9 2.3.3.9]~~ </~~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=6c6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c6o OCA], [https://pdbe.org/6c6o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c6o RCSB], [https://www.ebi.ac.uk/pdbsum/6c6o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c6o 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=6c6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c6o OCA], [~~http~~://pdbe.org/6c6o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c6o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c6o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c6o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A045ITM4_MYCTX A0A045ITM4_MYCTX]~~] Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA.[HAMAP-Rule:MF_00641~~][SAAS:SAAS00078445~~]	+	[https://www.uniprot.org/uniprot/MASZ_MYCTU MASZ_MYCTU] Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA (By similarity).[HAMAP-Rule:MF_00641]
	<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: ~~Malate synthase~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Krieger~~, I V~~]]	+	[[Category: Krieger IV]]
-	[[Category: Sacchettini~~, J C]]~~	+	[[Category: Sacchettini JC]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Acetyltransferase]]~~	+
-	~~[[Category: Tbsgc]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-transferase inhibitor complex~~]]	+

OCA at 09:31, 18 December 2019

OCA — Wed, 18 Dec 2019 09:31:44 GMT

←Older revision		Revision as of 09:31, 18 December 2019
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	==Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-Br-4-OH-phenyldiketoacid==		==Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-Br-4-OH-phenyldiketoacid==
-	<StructureSection load='6c6o' size='340' side='right' caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='6c6o' size='340' side='right'caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C6O FirstGlance]. <br>		<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C6O FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6c6o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6c6o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Malate synthase 3D structures\|Malate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Malate synthase]]		[[Category: Malate synthase]]
	[[Category: Krieger, I V]]		[[Category: Krieger, I V]]

OCA at 07:11, 31 October 2018

OCA — Wed, 31 Oct 2018 07:11:22 GMT

←Older revision		Revision as of 07:11, 31 October 2018
Line 3:		Line 3:
	<StructureSection load='6c6o' size='340' side='right' caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6c6o' size='340' side='right' caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C6O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C6O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ENG:(2Z)-4-(2-bromo-4-hydroxyphenyl)-2-hydroxy-4-oxobut-2-enoic+acid'>ENG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ENG:(2Z)-4-(2-bromo-4-hydroxyphenyl)-2-hydroxy-4-oxobut-2-enoic+acid'>ENG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glcB ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_synthase Malate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.3.9 2.3.3.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_synthase Malate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.3.9 2.3.3.9] </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=6c6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c6o OCA], [http://pdbe.org/6c6o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c6o RCSB], [http://www.ebi.ac.uk/pdbsum/6c6o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c6o 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=6c6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c6o OCA], [http://pdbe.org/6c6o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c6o RCSB], [http://www.ebi.ac.uk/pdbsum/6c6o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c6o ProSAT]</span></td></tr>

OCA at 10:05, 5 September 2018

OCA — Wed, 05 Sep 2018 10:05:54 GMT

←Older revision		Revision as of 10:05, 5 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6c6o is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-Br-4-OH-phenyldiketoacid==
		+	<StructureSection load='6c6o' size='340' side='right' caption='[[6c6o]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6c6o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C6O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C6O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ENG:(2Z)-4-(2-bromo-4-hydroxyphenyl)-2-hydroxy-4-oxobut-2-enoic+acid'>ENG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_synthase Malate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.3.9 2.3.3.9] </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=6c6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c6o OCA], [http://pdbe.org/6c6o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c6o RCSB], [http://www.ebi.ac.uk/pdbsum/6c6o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c6o ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A045ITM4_MYCTX A0A045ITM4_MYCTX]] Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA.[HAMAP-Rule:MF_00641][SAAS:SAAS00078445]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human infection by Mycobacterium tuberculosis (Mtb) continues to be a global epidemic. Computer-aided drug design (CADD) methods are used to accelerate traditional drug discovery efforts. One non-covalent interaction that is being increasingly identified in biological systems but is neglected in CADD is the anion-pi interaction. The study reported herein supports the conclusion that anion-pi interactions play a central role in directing the binding of phenyl-diketo acid (PDKA) inhibitors to malate synthase (GlcB), an enzyme required for Mycobacterium tuberculosis virulence. Using density functional theory methods (M06-2X/6-31+G(d)), a GlcB active site template was developed for a predictive model through a comparative analysis of PDKA-bound GlcB crystal structures. The active site model includes the PDKA molecule and the protein determinants of the electrostatic, hydrogen-bonding, and anion-pi interactions involved in binding. The predictive model accurately determines the Asp 633-PDKA structural position upon binding, and precisely predicts the relative binding enthalpies of a series of 2-ortho halide-PDKAs to GlcB. A screening model was also developed to efficiently assess the propensity of each PDKA analog to participate in an anion-pi interaction; this method is in good agreement with both the predictive model and the experimental binding enthalpies for the 2-ortho halide-PDKAs. With the screening and predictive models in hand, we have developed an efficient method for computationally screening and evaluating the binding enthalpy of variously substituted PDKA molecules. This study serves to illustrate the contribution of this overlooked interaction to binding affinity and demonstrates the importance of integrating anion-pi interactions into structure-based CADD.

-	~~Authors~~: ~~Krieger~~, I~~.V.~~, Sacchettini, J.C.~~, TB Structural Genomics Consortium (TBSGC)~~	+	Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.,Ellenbarger J, Krieger I, Huang HL, Gomez-Coca S, Ioerger TR, Sacchettini JC, Wheeler SE, Dunbar KR J Chem Inf Model. 2018 Aug 23. doi: 10.1021/acs.jcim.8b00417. PMID:30137983<ref>PMID:30137983</ref>

-	~~Description: Crystal structure~~ of ~~Mycobacterium tuberculosis malate synthase in complex with 2~~-Br-~~4-OH-phenyldiketoacid~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Sacchettini, J.C]]	+	<div class="pdbe-citations 6c6o" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Krieger, I.V~~]]	+	== References ==
-	[[Category: ~~Tb Structural Genomics Consortium (~~Tbsgc)]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Malate synthase]]
		+	[[Category: Krieger, I V]]
		+	[[Category: Sacchettini, J C]]
		+	[[Category: Structural genomic]]
		+	[[Category: Acetyltransferase]]
		+	[[Category: Tbsgc]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-transferase inhibitor complex]]

OCA: Protected "6c6o" [edit=sysop:move=sysop]

OCA — Wed, 31 Jan 2018 04:47:30 GMT

Protected "6c6o" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:47, 31 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c6o is ON HOLD until Paper Publication Authors: Krieger, I.V., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC) Description: Crystal s...

OCA — Wed, 31 Jan 2018 04:47:29 GMT

New page: '''Unreleased structure''' The entry 6c6o is ON HOLD until Paper Publication Authors: Krieger, I.V., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC) Description: Crystal s...

New page

'''Unreleased structure'''

The entry 6c6o is ON HOLD until Paper Publication

Authors: Krieger, I.V., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Description: Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-Br-4-OH-phenyldiketoacid
[[Category: Unreleased Structures]]
[[Category: Sacchettini, J.C]]
[[Category: Krieger, I.V]]
[[Category: Tb Structural Genomics Consortium (Tbsgc)]]