3dva: Difference between revisions

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 ==Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex==
-<StructureSection load='3dva' size='340' side='right' caption='[[3dva]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+<StructureSection load='3dva' size='340' side='right'caption='[[3dva]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dva]] is a 10 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=3DVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DVA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dva]] is a 10 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=3DVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DVA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPW:2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TPW</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]] 2.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w85|1w85]], [[1w88|1w88]], [[3duf|3duf]], [[3dv0|3dv0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPW:2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TPW</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus]), pdhB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus]), pdhC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</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=3dva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dva OCA], [https://pdbe.org/3dva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dva RCSB], [https://www.ebi.ac.uk/pdbsum/3dva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dva ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_(acetyl-transferring) Pyruvate dehydrogenase (acetyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1] </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=3dva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dva OCA], [http://pdbe.org/3dva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dva RCSB], [http://www.ebi.ac.uk/pdbsum/3dva PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ODP2_GEOSE ODP2_GEOSE]] The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). [[http://www.uniprot.org/uniprot/ODPB_GEOSE ODPB_GEOSE]] The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).
+[https://www.uniprot.org/uniprot/ODPB_GEOSE ODPB_GEOSE] The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).
 == 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/dv/3dva_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/3dva_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Dihydrolipoamide acetyltransferase|Dihydrolipoamide acetyltransferase]]
+*[[Dihydrolipoamide acetyltransferase 3D structures|Dihydrolipoamide acetyltransferase 3D structures]]
-*[[Pyruvate dehydrogenase|Pyruvate dehydrogenase]]
+*[[Pyruvate dehydrogenase 3D structures|Pyruvate dehydrogenase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 38: @@
 </StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Frank, R A.W]]
+[[Category: Large Structures]]
-[[Category: Leeper, F J]]
+[[Category: Frank RAW]]
-[[Category: Luisi, B F]]
+[[Category: Leeper FJ]]
-[[Category: Pei, X Y]]
+[[Category: Luisi BF]]
-[[Category: Titman, C M]]
+[[Category: Pei XY]]
-[[Category: Acetyl transferase]]
+[[Category: Titman CM]]
-[[Category: Acyltransferase]]
-[[Category: Dehydrogenase]]
-[[Category: Dihydrolipoyl]]
-[[Category: Glycolysis]]
-[[Category: Multienzyme complex]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase-transferase complex]]
-[[Category: Phosphoprotein]]
-[[Category: Pyruvate]]
-[[Category: Thiamine pyrophosphate]]
-[[Category: Transferase]]