3qdf - Revision history

OCA at 11:41, 14 March 2024

2024-03-14T11:41:33Z

←Older revision		Revision as of 11:41, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3qdf' size='340' side='right'caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3qdf' size='340' side='right'caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Mycmm Mycmm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QDF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_marinum_M Mycobacterium marinum M]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QDF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.05Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MMAR_1718 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~216594 MYCMM])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </~~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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [https://pdbe.org/3qdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [https://www.ebi.ac.uk/pdbsum/3qdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdf ProSAT]</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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [https://pdbe.org/3qdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [https://www.ebi.ac.uk/pdbsum/3qdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdf ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/B2HIH3_MYCMM B2HIH3_MYCMM]
-	High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Calpha RMSD <1 A, >85% side chain identity, and >/=80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.	+
-		+
-	Increasing the structural coverage of tuberculosis drug targets.,Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ Tuberculosis (Edinb). 2014 Dec 19. pii: ~~S1472-9792(14)20565-8. doi:, 10.1016~~/~~j.tube.2014.12.003. PMID:25613812<ref>PMID:25613812<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3qdf" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Mycmm]]~~	+	[[Category: Mycobacterium marinum M]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: 2-hydroxyhepta-2]]~~	+
-	~~[[Category: 2-oxohept-3-enedioate]]~~	+
-	~~[[Category: 4-diene-1]]~~	+
-	~~[[Category: 4-dienedioate]]~~	+
-	~~[[Category: 7-dioate isomerase]]~~	+
-	~~[[Category: Homoprotocatechuate degradative pathway]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	[[Category: Mycobacterium]]	+
-	~~[[Category: Non-pathogenic species]]~~	+
-	~~[[Category: Rv2993c ortholog]]~~	+
-	~~[[Category: Ssgcid]]~~	+
-	~~[[Category: Tuberculosis~~]]	+

OCA at 06:03, 8 June 2022

2022-06-08T06:03:30Z

←Older revision		Revision as of 06:03, 8 June 2022
Line 1:		Line 1:

	==Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum==		==Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum==
-	<StructureSection load='3qdf' size='340' side='right' caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='3qdf' size='340' side='right'caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mycmm Mycmm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QDF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycmm Mycmm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QDF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216594 MYCMM])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216594 MYCMM])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [~~http~~://pdbe.org/3qdf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qdf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdf ProSAT]</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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [https://pdbe.org/3qdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [https://www.ebi.ac.uk/pdbsum/3qdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]		[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]
		+	[[Category: Large Structures]]
	[[Category: Mycmm]]		[[Category: Mycmm]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 18:52, 1 February 2017

2017-02-01T18:52:33Z

←Older revision		Revision as of 18:52, 1 February 2017
Line 1:		Line 1:
		+
	==Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum==		==Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum==
	<StructureSection load='3qdf' size='340' side='right' caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3qdf' size='340' side='right' caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216594 MYCMM])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216594 MYCMM])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [http://www.ebi.ac.uk/pdbsum/3qdf PDBsum]</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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [http://pdbe.org/3qdf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [http://www.ebi.ac.uk/pdbsum/3qdf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3qdf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:26, 22 April 2015

2015-04-22T07:26:24Z

←Older revision		Revision as of 07:26, 22 April 2015
Line 2:		Line 2:
	<StructureSection load='3qdf' size='340' side='right' caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='3qdf' size='340' side='right' caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_marinum Mycobacterium marinum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QDF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycmm Mycmm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QDF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1781 Mycobacterium marinum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216594 MYCMM])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [http://www.ebi.ac.uk/pdbsum/3qdf PDBsum]</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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [http://www.ebi.ac.uk/pdbsum/3qdf PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Calpha RMSD <1 A, >85% side chain identity, and >/=80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
		+
		+	Increasing the structural coverage of tuberculosis drug targets.,Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ Tuberculosis (Edinb). 2014 Dec 19. pii: S1472-9792(14)20565-8. doi:, 10.1016/j.tube.2014.12.003. PMID:25613812<ref>PMID:25613812</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]		[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]
-	[[Category: ~~Mycobacterium marinum~~]]	+	[[Category: Mycmm]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: 2-hydroxyhepta-2]]		[[Category: 2-hydroxyhepta-2]]

OCA at 11:26, 20 January 2015

2015-01-20T11:26:52Z

←Older revision		Revision as of 11:26, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3qdf\| PDB=3qdf \| SCENE= }}~~	+	==Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum==
-	===Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum===	+	<StructureSection load='3qdf' size='340' side='right' caption='[[3qdf]], [[Resolution\|resolution]] 2.05Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[3qdf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_marinum Mycobacterium marinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QDF FirstGlance]. <br>
-	[[3qdf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_marinum Mycobacterium marinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMAR_1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1781 Mycobacterium marinum])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-carboxymethyl-2-hydroxymuconate_Delta-isomerase 5-carboxymethyl-2-hydroxymuconate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.10 5.3.3.10] </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=3qdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qdf RCSB], [http://www.ebi.ac.uk/pdbsum/3qdf PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]		[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]
	[[Category: Mycobacterium marinum]]		[[Category: Mycobacterium marinum]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.~~]]	+	[[Category: Structural genomic]]
	[[Category: 2-hydroxyhepta-2]]		[[Category: 2-hydroxyhepta-2]]
	[[Category: 2-oxohept-3-enedioate]]		[[Category: 2-oxohept-3-enedioate]]
Line 17:		Line 23:
	[[Category: Non-pathogenic species]]		[[Category: Non-pathogenic species]]
	[[Category: Rv2993c ortholog]]		[[Category: Rv2993c ortholog]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Tuberculosis]]		[[Category: Tuberculosis]]

OCA at 08:34, 8 May 2013

2013-05-08T08:34:26Z

←Older revision		Revision as of 08:34, 8 May 2013
Line 1:		Line 1:
-	[[Image:3qdf.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3qdf", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3qdf\| PDB=3qdf \| SCENE= }}		{{STRUCTURE_3qdf\| PDB=3qdf \| SCENE= }}
-
	===Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum===		===Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum===
-

	==About this Structure==		==About this Structure==
Line 17:		Line 7:
	[[Category: Mycobacterium marinum]]		[[Category: Mycobacterium marinum]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: 2-hydroxyhepta-2]]
		+	[[Category: 2-oxohept-3-enedioate]]
		+	[[Category: 4-diene-1]]
		+	[[Category: 4-dienedioate]]
		+	[[Category: 7-dioate isomerase]]
		+	[[Category: Homoprotocatechuate degradative pathway]]
		+	[[Category: Isomerase]]
		+	[[Category: Mycobacterium]]
		+	[[Category: Non-pathogenic species]]
		+	[[Category: Rv2993c ortholog]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]
		+	[[Category: Tuberculosis]]

OCA at 06:35, 2 February 2011

2011-02-02T06:35:30Z

←Older revision		Revision as of 06:35, 2 February 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3qdf.jpg\|left\|200px]]

-	The ~~entry 3qdf~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qdf", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qdf\| PDB=3qdf \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum===

-	~~Description: Crystal~~ structure ~~of 2~~-~~hydroxyhepta~~-2,4-~~diene~~-~~1,7-dioate~~ isomerase ~~from~~ Mycobacterium marinum	+
		+	==About this Structure==
		+	[[3qdf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_marinum Mycobacterium marinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDF OCA].
		+	[[Category: 5-carboxymethyl-2-hydroxymuconate Delta-isomerase]]
		+	[[Category: Mycobacterium marinum]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]

OCA: Protected "3qdf" [edit=sysop:move=sysop]

2011-01-26T12:46:44Z

Protected "3qdf" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:46, 26 January 2011

OCA: New page: '''Unreleased structure''' The entry 3qdf is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of 2-hydroxyhepta-2,4-di...

2011-01-26T12:46:44Z

New page: '''Unreleased structure''' The entry 3qdf is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of 2-hydroxyhepta-2,4-di...

New page

'''Unreleased structure'''

The entry 3qdf is ON HOLD

Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Description: Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum