3bvd: Difference between revisions

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 ==Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min==
-<StructureSection load='3bvd' size='340' side='right' caption='[[3bvd]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
+<StructureSection load='3bvd' size='340' side='right'caption='[[3bvd]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bvd]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BVD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bvd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BVD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</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]] 3.37&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qpd|2qpd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=3bvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvd OCA], [https://pdbe.org/3bvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvd RCSB], [https://www.ebi.ac.uk/pdbsum/3bvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvd 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/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3bvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvd OCA], [http://pdbe.org/3bvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bvd RCSB], [http://www.ebi.ac.uk/pdbsum/3bvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/COX2_THET8 COX2_THET8]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
+[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8]
 == 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/bv/3bvd_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/3bvd_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 29: @@
 </div>
 <div class="pdbe-citations 3bvd" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cytochrome-c oxidase]]
+[[Category: Large Structures]]
-[[Category: Thermus thermophilus]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Fee, J A]]
+[[Category: Fee JA]]
-[[Category: Luna, V M]]
+[[Category: Luna VM]]
-[[Category: Stout, C D]]
+[[Category: Stout CD]]
-[[Category: Copper]]
-[[Category: Cytochrome ba3 oxidase]]
-[[Category: Electron transport]]
-[[Category: Formylation]]
-[[Category: Heme]]
-[[Category: Hydrogen ion transport]]
-[[Category: Integral membrane protein]]
-[[Category: Ion transport]]
-[[Category: Iron]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Respiratory chain]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-[[Category: Xenon]]