3ddn - Revision history

OCA at 15:08, 1 November 2023

2023-11-01T15:08:05Z

←Older revision		Revision as of 15:08, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3ddn' size='340' side='right'caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3ddn' size='340' side='right'caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HPV:2~~-~~OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>~~, ~~<scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1ygy\|1ygy]], [[3dc2\|3dc2]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>serA1 ([https://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~~'>~~[https://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95]~~ </~~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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [https://pdbe.org/3ddn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [https://www.ebi.ac.uk/pdbsum/3ddn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddn 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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [https://pdbe.org/3ddn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [https://www.ebi.ac.uk/pdbsum/3ddn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SERA_MYCTU SERA_MYCTU]
	== 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: ~~Phosphoglycerate dehydrogenase~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Dey, S]]	+	[[Category: Dey S]]
-	[[Category: Sacchettini~~, J C]]~~	+	[[Category: Sacchettini JC]]
-	~~[[Category: Amino-acid biosynthesis]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Serine biosynthesis~~]]	+

OCA at 07:56, 9 February 2022

2022-02-09T07:56:27Z

←Older revision		Revision as of 07:56, 9 February 2022
Line 1:		Line 1:

	==Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis==		==Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis==
-	<StructureSection load='3ddn' size='340' side='right' caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3ddn' size='340' side='right'caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DDN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ygy\|1ygy]], [[3dc2\|3dc2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ygy\|1ygy]], [[3dc2\|3dc2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([~~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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([https://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/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [~~http~~://pdbe.org/3ddn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ddn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddn 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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [https://pdbe.org/3ddn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [https://www.ebi.ac.uk/pdbsum/3ddn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]
	[[Category: Dey, S]]		[[Category: Dey, S]]

OCA at 09:37, 14 November 2018

2018-11-14T09:37:23Z

←Older revision		Revision as of 09:37, 14 November 2018
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddn_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 20:56, 11 August 2016

2016-08-11T20:56:15Z

←Older revision		Revision as of 20:56, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis==		==Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis==
	<StructureSection load='3ddn' size='340' side='right' caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3ddn' size='340' side='right' caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ygy\|1ygy]], [[3dc2\|3dc2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ygy\|1ygy]], [[3dc2\|3dc2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([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/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [http://www.ebi.ac.uk/pdbsum/3ddn 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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [http://pdbe.org/3ddn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [http://www.ebi.ac.uk/pdbsum/3ddn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		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=3ddn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		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 3ddn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]
	[[Category: Dey, S]]		[[Category: Dey, S]]

OCA at 11:27, 20 January 2015

2015-01-20T11:27:45Z

←Older revision		Revision as of 11:27, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDN FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ygy\|1ygy]], [[3dc2\|3dc2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ygy\|1ygy]], [[3dc2\|3dc2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [http://www.ebi.ac.uk/pdbsum/3ddn 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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [http://www.ebi.ac.uk/pdbsum/3ddn PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]
-	[[Category: Dey, S.]]	+	[[Category: Dey, S]]
-	[[Category: Sacchettini, J C.]]	+	[[Category: Sacchettini, J C]]
	[[Category: Amino-acid biosynthesis]]		[[Category: Amino-acid biosynthesis]]
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Phosphoglycerate dehydrogenase]]
	[[Category: Serine biosynthesis]]		[[Category: Serine biosynthesis]]

OCA at 13:10, 29 September 2014

2014-09-29T13:10:56Z

←Older revision		Revision as of 13:10, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3ddn.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis==
		+	<StructureSection load='3ddn' size='340' side='right' caption='[[3ddn]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ddn]] is a 2 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=3DDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPV:2-OXO-3-(PHOSPHONOOXY)PROPANOIC+ACID'>HPV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ygy\|1ygy]], [[3dc2\|3dc2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">serA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95] </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=3ddn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddn RCSB], [http://www.ebi.ac.uk/pdbsum/3ddn 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/dd/3ddn_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 ==
		+	The crystal structure of Mycobacterium tuberculosis d-3-phosphoglycerate dehydrogenase has been solved with bound effector, l-serine, and substrate, hydroxypyruvic acid phosphate, at resolutions of 2.7 and 2.4 A, respectively. The subunits display the same extreme asymmetry as seen in the apo-structure and provide insight into the mode of serine binding and closure of the active site. Mutagenesis studies confirm the identity of the main residues involved in serine binding and suggest that the poly glycine stretch in the loop that contains the locus for the 160 degrees rotation that leads to subunit asymmetry may have a larger role in folding than in catalysis. The lack of electron density for the cofactor, NADH, in any of the crystals examined led us to study binding by stopped flow kinetic analysis. The kinetic data suggest that productive NADH binding, that would support catalytic turnover, is dependent on the presence of substrate. This observation, along with the binding of substrate in the active site, but in an unproductive conformation, suggests a possible mechanism where initial binding of substrate leads to enhanced interaction with cofactor accompanied by a rearrangement of catalytically critical residue side chains. Furthermore, comparison to the structure of a truncated form of human d-3-phosphoglycerate dehydrogenase with cofactor and a substrate analog, provides insight into the conformational changes that occur during catalysis.

-	~~{{STRUCTURE_3ddn\| PDB=3ddn \| SCENE= }}~~	+	Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase.,Dey S, Burton RL, Grant GA, Sacchettini JC Biochemistry. 2008 Aug 12;47(32):8271-82. Epub 2008 Jul 16. PMID:18627175<ref>PMID:18627175</ref>

-	~~===Crystal structure~~ of ~~hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18627175}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ddn]] is a 2 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=3DDN OCA].~~	+

	==See Also==		==See Also==
	*[[Phosphoglycerate dehydrogenase\|Phosphoglycerate dehydrogenase]]		*[[Phosphoglycerate dehydrogenase\|Phosphoglycerate dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018627175<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]

OCA at 18:01, 20 October 2012

2012-10-20T18:01:08Z

←Older revision		Revision as of 18:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3ddn]] is a 2 chain structure ~~of [[Phosphoglycerate dehydrogenase]]~~ 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=3DDN OCA].	+	[[3ddn]] is a 2 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=3DDN OCA].

	==See Also==		==See Also==

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

2012-07-27T02:43:36Z

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

←Older revision

Revision as of 02:43, 27 July 2012

OCA at 02:43, 27 July 2012

2012-07-27T02:43:35Z

←Older revision		Revision as of 02:43, 27 July 2012
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-	{{Seed}}
	[[Image:3ddn.png\|left\|200px]]		[[Image:3ddn.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3ddn\| PDB=3ddn \| SCENE= }}		{{STRUCTURE_3ddn\| PDB=3ddn \| SCENE= }}

	===Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis===		===Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18627175}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_18627175}}		{{ABSTRACT_PUBMED_18627175}}

	==About this Structure==		==About this Structure==
-	~~3DDN~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=3DDN OCA].	+	[[3ddn]] is a 2 chain structure of [[Phosphoglycerate dehydrogenase]] 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=3DDN OCA].
		+
		+	==See Also==
		+	*[[Phosphoglycerate dehydrogenase\|Phosphoglycerate dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18627175~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018627175</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]
Line 33:		Line 24:
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]
	[[Category: Serine biosynthesis]]		[[Category: Serine biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:10:36 2009''

OCA at 17:10, 17 February 2009

2009-02-17T17:10:39Z

←Older revision		Revision as of 17:10, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3DDN is a ~~[[Single protein]]~~ structure of ~~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=3DDN OCA].	+	3DDN is a 2 chains structure of sequences 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=3DDN OCA].

	==Reference==		==Reference==
-	Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase., Dey S, Burton RL, Grant GA, Sacchettini JC, Biochemistry. 2008 Aug 12;47(32):8271-82. Epub 2008 Jul 16. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18627175 18627175]~~	+	<ref group="xtra">PMID:18627175</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Phosphoglycerate dehydrogenase]]		[[Category: Phosphoglycerate dehydrogenase]]
-	[[Category: Single protein]]
	[[Category: Dey, S.]]		[[Category: Dey, S.]]
	[[Category: Sacchettini, J C.]]		[[Category: Sacchettini, J C.]]
Line 35:		Line 34:
	[[Category: Serine biosynthesis]]		[[Category: Serine biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug 20 11~~:31:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:10:36 2009''