1lde: Difference between revisions

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 ==HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE==
-<StructureSection load='1lde' size='340' side='right' caption='[[1lde]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1lde' size='340' side='right'caption='[[1lde]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1lde]] is a 4 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=1LDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LDE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1lde]] is a 4 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=1LDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LDE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FPI:N-FORMYLPIPERIDINE'>FPI</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bto|3bto]], [[1ldy|1ldy]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FPI:N-FORMYLPIPERIDINE'>FPI</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1lde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lde OCA], [https://pdbe.org/1lde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lde RCSB], [https://www.ebi.ac.uk/pdbsum/1lde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lde 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=1lde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lde RCSB], [http://www.ebi.ac.uk/pdbsum/1lde PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]
 == 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/1lde_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/1lde_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].
+</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=1lde ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Amides are analogs of aldehydes and potent inhibitors of liver alcohol dehydrogenases. They can be used for structural studies and for inhibiting the metabolism of alcohols that form toxic products. We studied N-alkyl amides that bind to the enzyme-NADH complex and act as uncompetitive inhibitors against varied concentrations of ethanol (millimolar Kii values, at pH 8 and 25 degrees C): N-propylacetamide (16), delta-valerolactam (1.6), N-formylpiperidine (0.14), N-isobutylformamide (0.028), N-(cyclohexylmethyl)-formamide (0.011), and N-cyclohexylformamide (0.0087). The lower affinity of delta-valerolactam and N-propylacetamide can be explained by steric hindrance with Phe93 of the enzyme. Replacing Phe93 with Ala in the S48T/F93A mutated enzyme, which resembles the natural alpha-isoenzyme of primates, improved binding of delta-valerolactam by 210-fold. The structures of horse liver enzyme complexed with NADH and N-cyclohexylformamide or N-formylpiperidine were determined by X-ray crystallography at 2.5 A resolution. In both complexes, the carbonyl oxygens of the inhibitors bind to the catalytic zinc and form a hydrogen bond to the hydroxyl group of Ser48 of the enzyme. The six-membered rings bind in overlapping, but rotated, positions that optimize hydrophobic interactions. The binding modes of the unreactive formamides appear to resemble the Michaelis complexes of the analogous substrates, with the re face of the carbonyl carbon suitably positioned to accept a hydrogen from NADH.
-Binding of formamides to liver alcohol dehydrogenase.,Ramaswamy S, Scholze M, Plapp BV Biochemistry. 1997 Mar 25;36(12):3522-7. PMID:9132002<ref>PMID:9132002</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Alcohol dehydrogenase|Alcohol dehydrogenase]]
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Alcohol dehydrogenase]]
 [[Category: Equus caballus]]
-[[Category: Plapp, B V]]
+[[Category: Large Structures]]
-[[Category: Ramaswamy, S]]
+[[Category: Plapp BV]]
-[[Category: Alcohol]]
+[[Category: Ramaswamy S]]
-[[Category: Dehydrogenase]]
-[[Category: Formamide]]
-[[Category: Nicotinamide coenzyme]]
-[[Category: Oxidoreductase]]