2c9d - Revision history

OCA at 14:10, 13 December 2023

OCA — Wed, 13 Dec 2023 14:10:11 GMT

←Older revision		Revision as of 14:10, 13 December 2023
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	<StructureSection load='2c9d' size='340' side='right'caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2c9d' size='340' side='right'caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2c9d]] is a 10 chain structure with sequence from [https://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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2c9d]] is a 10 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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</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]] 2.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [https://pdbe.org/2c9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [https://www.ebi.ac.uk/pdbsum/2c9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9d 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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [https://pdbe.org/2c9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [https://www.ebi.ac.uk/pdbsum/2c9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>	+	[https://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Riboflavin synthase]]
-	[[Category: Bacher, A]]
-	[[Category: Cushman, M]]
-	[[Category: Fischer, M]]
-	[[Category: Haase, I]]
-	[[Category: Illarionov, B]]
-	[[Category: Jin, G]]
-	[[Category: Ladenstein, R]]
-	[[Category: Morgunova, E]]
-	[[Category: Inhibitor binding]]
-	[[Category: Lumazine synthase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Riboflavin biosynthesis~~]]	+	[[Category: Bacher A]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Cushman M]]
		+	[[Category: Fischer M]]
		+	[[Category: Haase I]]
		+	[[Category: Illarionov B]]
		+	[[Category: Jin G]]
		+	[[Category: Ladenstein R]]
		+	[[Category: Morgunova E]]

OCA at 11:43, 3 February 2021

OCA — Wed, 03 Feb 2021 11:43:17 GMT

←Older revision		Revision as of 11:43, 3 February 2021
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	<StructureSection load='2c9d' size='340' side='right'caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2c9d' size='340' side='right'caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2c9d]] is a 10 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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2C9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2c9d]] is a 10 chain structure with sequence from [https://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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [~~http~~://pdbe.org/2c9d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2c9d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9d 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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [https://pdbe.org/2c9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [https://www.ebi.ac.uk/pdbsum/2c9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>	+	[[https://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:34, 10 April 2019

OCA — Wed, 10 Apr 2019 07:34:34 GMT

←Older revision		Revision as of 07:34, 10 April 2019
Line 1:		Line 1:

	==Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE==		==Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE==
-	<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='2c9d' size='340' side='right'caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c9d]] is a 10 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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c9d]] is a 10 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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]

OCA at 06:01, 20 June 2018

OCA — Wed, 20 Jun 2018 06:01:40 GMT

←Older revision		Revision as of 06:01, 20 June 2018
Line 1:		Line 1:

-	==~~LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO~~ 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)~~hexaNE~~ 1-PHOSPHATE==	+	==Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE==
	<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 08:38, 23 May 2018

OCA — Wed, 23 May 2018 08:38:31 GMT

←Older revision		Revision as of 08:38, 23 May 2018
Line 1:		Line 1:
-	==LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) ~~HEXANE~~ 1-PHOSPHATE==	+
		+	==LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)hexaNE 1-PHOSPHATE==
	<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://pdbe.org/2c9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d 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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://pdbe.org/2c9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c9d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c9d_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 05:20, 10 February 2016

OCA — Wed, 10 Feb 2016 05:20:08 GMT

←Older revision		Revision as of 05:20, 10 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2c9d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:46, 11 September 2015

OCA — Fri, 11 Sep 2015 05:46:18 GMT

←Older revision		Revision as of 05:46, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2c9d]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2c9d]] is a 10 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=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d 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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://pdbe.org/2c9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2c9d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
Line 44:		Line 44:
	[[Category: Inhibitor binding]]		[[Category: Inhibitor binding]]
	[[Category: Lumazine synthase]]		[[Category: Lumazine synthase]]
		+	[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin biosynthesis]]		[[Category: Riboflavin biosynthesis]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 12:06, 25 December 2014

OCA — Thu, 25 Dec 2014 12:06:20 GMT

←Older revision		Revision as of 12:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c9d]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c9d]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d 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=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
-	[[Category: Bacher, A.]]	+	[[Category: Bacher, A]]
-	[[Category: Cushman, M.]]	+	[[Category: Cushman, M]]
-	[[Category: Fischer, M.]]	+	[[Category: Fischer, M]]
-	[[Category: Haase, I.]]	+	[[Category: Haase, I]]
-	[[Category: Illarionov, B.]]	+	[[Category: Illarionov, B]]
-	[[Category: Jin, G.]]	+	[[Category: Jin, G]]
-	[[Category: Ladenstein, R.]]	+	[[Category: Ladenstein, R]]
-	[[Category: Morgunova, E.]]	+	[[Category: Morgunova, E]]
	[[Category: Inhibitor binding]]		[[Category: Inhibitor binding]]
	[[Category: Lumazine synthase]]		[[Category: Lumazine synthase]]
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin biosynthesis]]		[[Category: Riboflavin biosynthesis]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:06, 3 October 2014

OCA — Fri, 03 Oct 2014 09:06:08 GMT

←Older revision		Revision as of 09:06, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2c9d\| PDB=2c9d \| SCENE= }}~~	+	==LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) HEXANE 1-PHOSPHATE==
-	===LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) HEXANE 1-PHOSPHATE===	+	<StructureSection load='2c9d' size='340' side='right' caption='[[2c9d]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_16984393}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2c9d]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL+)+HEXANE+1-PHOSPHATE'>PHR</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]], [[1w29\|1w29]], [[2c92\|2c92]], [[2c94\|2c94]], [[2c97\|2c97]], [[2c9b\|2c9b]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c9d RCSB], [http://www.ebi.ac.uk/pdbsum/2c9d PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c9d_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs. The substituted purinetrione compounds have demonstrated high affinity and specificity to lumazine synthase, which catalyzes the penultimate step of riboflavin biosynthesis in bacteria and plants. The structure of M. tuberculosis lumazine synthase in complex with five different inhibitor compounds is presented, together with studies of the binding reactions by isothermal titration calorimetry. The inhibitors showed the association constants in the micromolar range. The analysis of the structures demonstrated the specific features of the binding of different inhibitors. The comparison of the structures and binding modes of five different inhibitors allows us to propose the ribitylpurinetrione compounds with C4-C5 alkylphosphate chains as most promising leads for further development of therapeutic drugs against M. tuberculosis.

-	~~==Function==~~	+	Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from Mycobacterium tuberculosis.,Morgunova E, Illarionov B, Sambaiah T, Haase I, Bacher A, Cushman M, Fischer M, Ladenstein R FEBS J. 2006 Oct;273(20):4790-804. Epub 2006 Sep 19. PMID:16984393<ref>PMID:16984393</ref>
-	~~[[http://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes~~ the ~~formation~~ of 6,~~7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-~~(~~D-ribitylamino~~)~~uracil with 3,4~~-~~dihydroxy-2-butanone 4-phosphate~~. ~~This is the penultimate step in the biosynthesis of riboflavin~~.<ref>PMID:~~15723519~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2c9d]] is~~ a ~~10 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2C9D OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:016984393</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]

OCA at 08:37, 23 April 2014

OCA — Wed, 23 Apr 2014 08:37:41 GMT

←Older revision		Revision as of 08:37, 23 April 2014
Line 1:		Line 1:
-	[[Image:2c9d.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_2c9d", 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_2c9d\| PDB=2c9d \| SCENE= }}		{{STRUCTURE_2c9d\| PDB=2c9d \| SCENE= }}
-
	===LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) HEXANE 1-PHOSPHATE===		===LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) HEXANE 1-PHOSPHATE===
		+	{{ABSTRACT_PUBMED_16984393}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_16984393}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 16984393~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_16984393}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:016984393</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016984393</ref><references group="xtra"/><references/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]