5mdk: Difference between revisions

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 ==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)==
-<StructureSection load='5mdk' size='340' side='right' caption='[[5mdk]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='5mdk' size='340' side='right'caption='[[5mdk]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mdk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_eutropha_h16 Alcaligenes eutropha h16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mdk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator_H16 Cupriavidus necator H16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HOXG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16]), HOXK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [https://pdbe.org/5mdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [https://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk 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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [http://pdbe.org/5mdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [http://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. [[http://www.uniprot.org/uniprot/MBHS_CUPNH MBHS_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.
+[https://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
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 __TOC__
 </StructureSection>
-[[Category: Alcaligenes eutropha h16]]
+[[Category: Cupriavidus necator H16]]
-[[Category: Kalms, J]]
+[[Category: Large Structures]]
-[[Category: Scheerer, P]]
+[[Category: Kalms J]]
-[[Category: Schmidt, A]]
+[[Category: Scheerer P]]
-[[Category: Aerobic hydrogen bacteria]]
+[[Category: Schmidt A]]
-[[Category: As-isolated state]]
-[[Category: Bimetallic]]
-[[Category: Dehydrogenase]]
-[[Category: Dihydrogen]]
-[[Category: Fe-s cluster]]
-[[Category: Gas transport]]
-[[Category: Hydrogen catalysis]]
-[[Category: Hydrophobic tunnel]]
-[[Category: Knallgasbacteria]]
-[[Category: Membrane]]
-[[Category: Membrane bound]]
-[[Category: Metalloenzyme]]
-[[Category: Metalloprotein catalytic center]]
-[[Category: Native]]
-[[Category: Ni-fe active site]]
-[[Category: Oxidized state]]
-[[Category: Oxidoreductase]]
-[[Category: Oxygen tolerant hydrogenase]]
-[[Category: Proteobacteria]]
-[[Category: T-cluster]]