5kms - Revision history

OCA at 09:14, 25 October 2023

OCA — Wed, 25 Oct 2023 09:14:26 GMT

←Older revision		Revision as of 09:14, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [https://pdbe.org/5kms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [https://www.ebi.ac.uk/pdbsum/5kms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms 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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [https://pdbe.org/5kms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [https://www.ebi.ac.uk/pdbsum/5kms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:57, 29 March 2023

OCA — Wed, 29 Mar 2023 06:57:09 GMT

←Older revision		Revision as of 06:57, 29 March 2023
Line 3:		Line 3:
	<StructureSection load='5kms' size='340' side='right'caption='[[5kms]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5kms' size='340' side='right'caption='[[5kms]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caltt Caltt~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kmq\|5kmq]], [[5kmp\|5kmp]], [[5kmr\|5kmr]]</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [https://pdbe.org/5kms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [https://www.ebi.ac.uk/pdbsum/5kms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CathTA2_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=986075 CALTT])</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [~~http~~://pdbe.org/5kms PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kms PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F5L3B8_CALTT F5L3B8_CALTT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caltt~~]]	+	[[Category: Caldalkalibacillus thermarum TA2 A1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aragao, D]]	+	[[Category: Aragao D]]
-	[[Category: Cook~~, G M~~]]	+	[[Category: Cook GM]]
-	[[Category: Nakatani, Y]]	+	[[Category: Nakatani Y]]
-	~~[[Category: Nadh dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 06:28, 5 August 2020

OCA — Wed, 05 Aug 2020 06:28:17 GMT

←Older revision		Revision as of 06:28, 5 August 2020
Line 1:		Line 1:

	==The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.==		==The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.==
-	<StructureSection load='5kms' size='340' side='right' caption='[[5kms]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5kms' size='340' side='right'caption='[[5kms]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KMS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caltt Caltt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KMS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kmq\|5kmq]], [[5kmp\|5kmp]], [[5kmr\|5kmr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kmq\|5kmq]], [[5kmp\|5kmp]], [[5kmr\|5kmr]]</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [http://pdbe.org/5kms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [http://www.ebi.ac.uk/pdbsum/5kms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CathTA2_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=986075 CALTT])</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [http://pdbe.org/5kms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [http://www.ebi.ac.uk/pdbsum/5kms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caltt]]
		+	[[Category: Large Structures]]
	[[Category: Aragao, D]]		[[Category: Aragao, D]]
	[[Category: Cook, G M]]		[[Category: Cook, G M]]

OCA at 17:52, 1 February 2017

OCA — Wed, 01 Feb 2017 17:52:06 GMT

←Older revision		Revision as of 17:52, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5kms is ~~ON HOLD~~	+	==The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.==
		+	<StructureSection load='5kms' size='340' side='right' caption='[[5kms]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kms]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KMS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kmq\|5kmq]], [[5kmp\|5kmp]], [[5kmr\|5kmr]]</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=5kms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kms OCA], [http://pdbe.org/5kms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kms RCSB], [http://www.ebi.ac.uk/pdbsum/5kms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kms ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.

-	~~Authors~~: ~~Cook, G.M~~., ~~Aragao~~, D., ~~Nakatani~~, Y.	+	The mechanism of catalysis by type-II NADH:quinone oxidoreductases.,Blaza JN, Bridges HR, Aragao D, Dunn EA, Heikal A, Cook GM, Nakatani Y, Hirst J Sci Rep. 2017 Jan 9;7:40165. doi: 10.1038/srep40165. PMID:28067272<ref>PMID:28067272</ref>

-	~~Description: The structure~~ of ~~type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2~~.~~5 angstrom resolution~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5kms" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aragao, D]]		[[Category: Aragao, D]]
		+	[[Category: Cook, G M]]
	[[Category: Nakatani, Y]]		[[Category: Nakatani, Y]]
-	[[Category: ~~Cook, G.M~~]]	+	[[Category: Nadh dehydrogenase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA: Protected "5kms" [edit=sysop:move=sysop]

OCA — Wed, 13 Jul 2016 00:34:37 GMT

Protected "5kms" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:34, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kms is ON HOLD Authors: Cook, G.M., Aragao, D., Nakatani, Y. Description: The structure of type II NADH dehydrogenase from Caldalkalibacillus ther...

OCA — Wed, 13 Jul 2016 00:34:36 GMT

New page: '''Unreleased structure''' The entry 5kms is ON HOLD Authors: Cook, G.M., Aragao, D., Nakatani, Y. Description: The structure of type II NADH dehydrogenase from Caldalkalibacillus ther...

New page

'''Unreleased structure'''

The entry 5kms is ON HOLD

Authors: Cook, G.M., Aragao, D., Nakatani, Y.

Description: The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.
[[Category: Unreleased Structures]]
[[Category: Aragao, D]]
[[Category: Nakatani, Y]]
[[Category: Cook, G.M]]