5wed - Revision history

OCA at 10:06, 22 May 2024

OCA — Wed, 22 May 2024 10:06:20 GMT

←Older revision		Revision as of 10:06, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5wed]] 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=5WED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WED FirstGlance]. <br>		<table><tr><td colspan='2'>[[5wed]] 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=5WED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WED 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></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]] 2.15Å</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></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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [https://pdbe.org/5wed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [https://www.ebi.ac.uk/pdbsum/5wed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed 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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [https://pdbe.org/5wed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [https://www.ebi.ac.uk/pdbsum/5wed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:57, 29 March 2023

OCA — Wed, 29 Mar 2023 06:57:40 GMT

←Older revision		Revision as of 06:57, 29 March 2023
Line 3:		Line 3:
	<StructureSection load='5wed' size='340' side='right'caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5wed' size='340' side='right'caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wed]] 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=5WED OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wed]] 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=5WED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WED 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>~~</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></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]]</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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [https://pdbe.org/5wed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [https://www.ebi.ac.uk/pdbsum/5wed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [~~http~~://pdbe.org/5wed PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wed PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed 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: Dehydrogenase]]~~	+
-	~~[[Category: Membrane/cytoplasm]]~~	+
-	~~[[Category: Nucleotide binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 09:49, 1 January 2020

OCA — Wed, 01 Jan 2020 09:49:42 GMT

←Older revision		Revision as of 09:49, 1 January 2020
Line 1:		Line 1:

	==Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.15A resolution==		==Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.15A resolution==
-	<StructureSection load='5wed' size='340' side='right' caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5wed' size='340' side='right'caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wed]] is a 4 chain structure with sequence from [http://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=5WED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wed]] 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=5WED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WED 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></td></tr>		</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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]]</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 ~~Caldalkalibacillus thermarum TA2.A1~~])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [http://pdbe.org/5wed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [http://www.ebi.ac.uk/pdbsum/5wed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed ProSAT]</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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [http://pdbe.org/5wed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [http://www.ebi.ac.uk/pdbsum/5wed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caldalkalibacillus thermarum ta2 a1~~]]	+	[[Category: Caltt]]
		+	[[Category: Large Structures]]
	[[Category: Aragao, D]]		[[Category: Aragao, D]]
	[[Category: Cook, G M]]		[[Category: Cook, G M]]

OCA at 06:39, 18 April 2018

OCA — Wed, 18 Apr 2018 06:39:54 GMT

←Older revision		Revision as of 06:39, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5wed' size='340' side='right' caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5wed' size='340' side='right' caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wed]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wed]] is a 4 chain structure with sequence from [http://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=5WED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WED 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></td></tr>		</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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]]</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 Caldalkalibacillus thermarum TA2.A1])</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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [http://pdbe.org/5wed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [http://www.ebi.ac.uk/pdbsum/5wed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed ProSAT]</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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [http://pdbe.org/5wed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [http://www.ebi.ac.uk/pdbsum/5wed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5 A). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 A). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.
		+
		+	Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 A.,Nakatani Y, Jiao W, Aragao D, Shimaki Y, Petri J, Parker EJ, Cook GM Acta Crystallogr F Struct Biol Commun. 2017 Oct 1;73(Pt 10):541-549. doi:, 10.1107/S2053230X17013073. Epub 2017 Sep 23. PMID:28994401<ref>PMID:28994401</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5wed" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caldalkalibacillus thermarum ta2 a1]]
	[[Category: Aragao, D]]		[[Category: Aragao, D]]
	[[Category: Cook, G M]]		[[Category: Cook, G M]]

OCA at 07:18, 18 October 2017

OCA — Wed, 18 Oct 2017 07:18:15 GMT

←Older revision		Revision as of 07:18, 18 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wed is ~~ON HOLD until Paper Publication~~	+	==Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.15A resolution==
-		+	<StructureSection load='5wed' size='340' side='right' caption='[[5wed]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5wed]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WED FirstGlance]. <br>
-	~~Description~~:	+	</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></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]]</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=5wed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wed OCA], [http://pdbe.org/5wed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wed RCSB], [http://www.ebi.ac.uk/pdbsum/5wed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wed ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aragao, D]]
		+	[[Category: Cook, G M]]
		+	[[Category: Nakatani, Y]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Membrane/cytoplasm]]
		+	[[Category: Nucleotide binding]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

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

OCA — Wed, 27 Sep 2017 14:44:08 GMT

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

←Older revision

Revision as of 14:44, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wed is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 14:44:07 GMT

New page: '''Unreleased structure''' The entry 5wed is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5wed is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]