2ldb - Revision history

OCA at 09:46, 25 December 2024

2024-12-25T09:46:10Z

← Older revision		Revision as of 09:46, 25 December 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/2ldb_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/2ldb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 07:04, 27 September 2023

2023-09-27T07:04:54Z

← Older revision		Revision as of 07:04, 27 September 2023
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	<StructureSection load='2ldb' size='340' side='right'caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2ldb' size='340' side='right'caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LDB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3Å</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [https://pdbe.org/2ldb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [https://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb 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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [https://pdbe.org/2ldb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [https://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/LDH_GEOSE LDH_GEOSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 12980]]~~		[[Category: Geobacillus stearothermophilus]]
	~~[[Category: L-lactate dehydrogenase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Piontek, K]]		[[Category: Piontek K]]
	[[Category: Rossmann~~, M G~~]]		[[Category: Rossmann MG]]

OCA at 07:50, 9 February 2022

2022-02-09T07:50:48Z

← Older revision		Revision as of 07:50, 9 February 2022
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	<StructureSection load='2ldb' size='340' side='right'caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2ldb' size='340' side='right'caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2LDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LDB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [~~http~~://pdbe.org/2ldb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb 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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [https://pdbe.org/2ldb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [https://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:02, 6 May 2020

2020-05-06T07:02:43Z

← Older revision		Revision as of 07:02, 6 May 2020
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	==STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE==		==STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE==
	<StructureSection load='2ldb' size='340' side='right' caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2ldb' size='340' side='right'caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2LDB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://pdbe.org/2ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://pdbe.org/2ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Lactate ~~Dehydrogenase~~\|Lactate ~~Dehydrogenase~~]]		*[[Lactate dehydrogenase 3D structures\|Lactate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
	[[Category: L-lactate dehydrogenase]]		[[Category: L-lactate dehydrogenase]]
			[[Category: Large Structures]]
	[[Category: Piontek, K]]		[[Category: Piontek, K]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]

OCA at 19:39, 1 August 2018

2018-08-01T19:39:26Z

← Older revision		Revision as of 19:39, 1 August 2018
Line 1:		Line 1:

	==STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE==		==STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE==
	<StructureSection load='2ldb' size='340' side='right' caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2ldb' size='340' side='right' caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://pdbe.org/2ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb 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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://pdbe.org/2ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ldb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/2ldb_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/2ldb_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 22:56, 7 February 2016

2016-02-07T22:56:05Z

← Older revision		Revision as of 22:56, 7 February 2016
Line 15:		Line 15:
	<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=2ldb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:38, 10 September 2015

2015-09-10T05:38:05Z

← Older revision		Revision as of 05:38, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2ldb' size='340' side='right' caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2ldb' size='340' side='right' caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LDB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb 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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://pdbe.org/2ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2ldb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Geobacillus stearothermophilus~~]]		[[Category: Atcc 12980]]
	[[Category: L-lactate dehydrogenase]]		[[Category: L-lactate dehydrogenase]]
	[[Category: Piontek, K]]		[[Category: Piontek, K]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]

OCA at 16:41, 19 January 2015

2015-01-19T16:41:26Z

← Older revision		Revision as of 16:41, 19 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LDB FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb 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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: L-lactate dehydrogenase]]		[[Category: L-lactate dehydrogenase]]
	[[Category: Piontek, K.]]		[[Category: Piontek, K]]
	[[Category: Rossmann, M G.]]		[[Category: Rossmann, M G]]

OCA at 03:30, 29 September 2014

2014-09-29T03:30:58Z

← Older revision		Revision as of 03:30, 29 September 2014
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	[[Image:~~2ldb~~.~~png~~\|~~left~~\|~~200px~~]]		==STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE==
			<StructureSection load='2ldb' size='340' side='right' caption='[[2ldb]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LDB FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=2ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ldb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ldb RCSB], [http://www.ebi.ac.uk/pdbsum/2ldb 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/ld/2ldb_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 ==
			Structures have been determined of Bacillus stearothermophilus "apo" and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-bisphosphate. The "apo" lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 A to 3 A resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 A resolution data, in a restrained least-squares refinement in which the molecular symmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the "apo"-enzyme. Further refinement proceeded with the isomorphous holo-enzyme from Bacillus stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 A and 1.7 degrees r.m.s. deviation from idealized bond lengths and angles, respectively. Two sulfate ions per subunit were included in the final model of the "apo"-form--one at the substrate binding site and one close to the molecular P-axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the "apo" model. This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with nicotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose 1,6-bisphosphate were also analyzed.

	~~{{STRUCTURE_2ldb\| PDB=2ldb \| SCENE= }}~~		Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase.,Piontek K, Chakrabarti P, Schar HP, Rossmann MG, Zuber H Proteins. 1990;7(1):74-92. PMID:2330370<ref>PMID:2330370</ref>

	~~===STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_2330370}}~~

	~~==About this Structure==~~
	~~[[2ldb]] is~~ a ~~4 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2LDB OCA].~~

	==See Also==		==See Also==
	*[[Lactate Dehydrogenase\|Lactate Dehydrogenase]]		*[[Lactate Dehydrogenase\|Lactate Dehydrogenase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:002330370<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: L-lactate dehydrogenase]]		[[Category: L-lactate dehydrogenase]]
	[[Category: Piontek, K.]]		[[Category: Piontek, K.]]
	[[Category: Rossmann, M G.]]		[[Category: Rossmann, M G.]]

OCA at 08:05, 20 October 2012

2012-10-20T08:05:21Z

← Older revision		Revision as of 08:05, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2ldb]] is a 4 chain structure ~~of [[Lactate Dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA].		[[2ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LDB OCA].

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