5kje - Revision history

OCA at 10:02, 27 September 2023

OCA — Wed, 27 Sep 2023 10:02:04 GMT

←Older revision		Revision as of 10:02, 27 September 2023
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	<StructureSection load='5kje' size='340' side='right'caption='[[5kje]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='5kje' size='340' side='right'caption='[[5kje]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KJE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KJE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.26Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dwv\|4dwv]], [[5kcp\|5kcp]], [[5kcz\|5kcz]], [[5kj1\|5kj1]], [[5kj6\|5kj6]], [[5kjc\|5kjc]], [[5kjf\|5kjf]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=5kje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kje OCA], [https://pdbe.org/5kje PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kje RCSB], [https://www.ebi.ac.uk/pdbsum/5kje PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kje 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=5kje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kje OCA], [~~http~~://pdbe.org/5kje PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kje RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kje PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kje ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Plapp~~, B V]]~~	+	[[Category: Plapp BV]]
-	~~[[Category: Dynamic]]~~	+
-	~~[[Category: Michaelis analogue]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 12:17, 25 December 2019

OCA — Wed, 25 Dec 2019 12:17:41 GMT

←Older revision		Revision as of 12:17, 25 December 2019
Line 1:		Line 1:

	==F322L horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol==		==F322L horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol==
-	<StructureSection load='5kje' size='340' side='right' caption='[[5kje]], [[Resolution\|resolution]] 1.26Å' scene=''>	+	<StructureSection load='5kje' size='340' side='right'caption='[[5kje]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KJE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KJE FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5kje" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kje" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	[[Category: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
		+	[[Category: Large Structures]]
	[[Category: Plapp, B V]]		[[Category: Plapp, B V]]
	[[Category: Dynamic]]		[[Category: Dynamic]]

OCA at 05:55, 3 January 2018

OCA — Wed, 03 Jan 2018 05:55:57 GMT

←Older revision		Revision as of 05:55, 3 January 2018
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	<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=5kje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kje OCA], [http://pdbe.org/5kje PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kje RCSB], [http://www.ebi.ac.uk/pdbsum/5kje PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kje 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=5kje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kje OCA], [http://pdbe.org/5kje PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kje RCSB], [http://www.ebi.ac.uk/pdbsum/5kje PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kje ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The dynamics of enzyme catalysis range from the slow time scale ( approximately ms) for substrate binding and conformational changes to the fast time ( approximately ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220(V, L or F), V222I, and F322L enzymes complexed with NAD(+) and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly-expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis. This article is protected by copyright. All rights reserved.
		+
		+	Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis.,Shanmuganatham KK, Wallace RS, Lee AT, Plapp BV Protein Sci. 2017 Dec 22. doi: 10.1002/pro.3370. PMID:29271062<ref>PMID:29271062</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kje" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:00, 6 November 2017

OCA — Mon, 06 Nov 2017 13:00:27 GMT

←Older revision		Revision as of 13:00, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5kje' size='340' side='right' caption='[[5kje]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='5kje' size='340' side='right' caption='[[5kje]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KJE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KJE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dwv\|4dwv]], [[5kcp\|5kcp]], [[5kcz\|5kcz]], [[5kj1\|5kj1]], [[5kj6\|5kj6]], [[5kjc\|5kjc]], [[5kjf\|5kjf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dwv\|4dwv]], [[5kcp\|5kcp]], [[5kcz\|5kcz]], [[5kj1\|5kj1]], [[5kj6\|5kj6]], [[5kjc\|5kjc]], [[5kjf\|5kjf]]</td></tr>
Line 12:		Line 12:
	</StructureSection>		</StructureSection>
	[[Category: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
		+	[[Category: Equus caballus]]
	[[Category: Plapp, B V]]		[[Category: Plapp, B V]]
	[[Category: Dynamic]]		[[Category: Dynamic]]

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

OCA — Wed, 13 Jul 2016 18:05:04 GMT

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

←Older revision

Revision as of 18:05, 13 July 2016

OCA: New page: ==F322L horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol== == Structural highlights ==
<table><tr><td colspan='2'>[[5kje]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KJE OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KJE FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[4dwv|4dwv]], [[5kcp|5kcp]], [[5kcz|5kcz]], [[5kj1|5kj1]], [[5kj6|5kj6]], [[5kjc|5kjc]], [[5kjf|5kjf]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5kje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kje OCA], [http://pdbe.org/5kje PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kje RCSB], [http://www.ebi.ac.uk/pdbsum/5kje PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kje ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Alcohol dehydrogenase]]
[[Category: Plapp, B V]]
[[Category: Dynamic]]
[[Category: Michaelis analogue]]
[[Category: Oxidoreductase]]
[[Category: Rossmann fold]]