3bdj: Difference between revisions

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-[[Image:3bdj.png|left|200px]]
-<!--
+==Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor==
-The line below this paragraph, containing "STRUCTURE_3bdj", creates the "Structure Box" on the page.
+<StructureSection load='3bdj' size='340' side='right'caption='[[3bdj]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3bdj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BDJ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=141:OXYPURINOL'>141</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MOW:OXO(SULFANYL)MOLYBDENUM(IV)+ION'>MOW</scene>, <scene name='pdbligand=MTE:PHOSPHONIC+ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER'>MTE</scene></td></tr>
-{{STRUCTURE_3bdj|  PDB=3bdj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bdj OCA], [https://pdbe.org/3bdj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bdj RCSB], [https://www.ebi.ac.uk/pdbsum/3bdj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bdj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XDH_BOVIN XDH_BOVIN] Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species.
+== 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/bd/3bdj_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/main_output.php?pdb_ID=3bdj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Inhibitors of xanthine oxidoreductase block conversion of xanthine to uric acid and are therefore potentially useful for treatment of hyperuricemia or gout. We determined the crystal structure of reduced bovine milk xanthine oxidoreductase complexed with oxipurinol at 2.0 A resolution. Clear electron density was observed between the N2 nitrogen of oxipurinol and the molybdenum atom of the molybdopterin cofactor, indicating that oxipurinol coordinated directly to molybdenum. Oxipurinol forms hydrogen bonds with glutamate 802, arginine 880, and glutamate 1261, which have previously been shown to be essential for the enzyme reaction. We discuss possible differences in the hypouricemic effect of inhibitors, including allopurinol and newly developed inhibitors, based on their mode of binding in the crystal structures.
-===Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor===
+Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol.,Okamoto K, Eger BT, Nishino T, Pai EF, Nishino T Nucleosides Nucleotides Nucleic Acids. 2008 Jun;27(6):888-93. PMID:18600558<ref>PMID:18600558</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bdj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18600558}}, adds the Publication Abstract to the page
+*[[Xanthine dehydrogenase 3D structures|Xanthine dehydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18600558 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18600558}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3bdj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BDJ OCA].
-==Reference==
-<ref group="xtra">PMID:18600558</ref><ref group="xtra">PMID:11796116</ref><ref group="xtra">PMID:15148401</ref><ref group="xtra">PMID:15190124</ref><ref group="xtra">PMID:12421831</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Eger, B T.]]
+[[Category: Large Structures]]
-[[Category: Nishino, T.]]
+[[Category: Eger BT]]
-[[Category: Okamoto, K.]]
+[[Category: Nishino T]]
-[[Category: Pai, E F.]]
+[[Category: Okamoto K]]
-[[Category: 2fe-2]]
+[[Category: Pai EF]]
-[[Category: Allopurinol]]
-[[Category: Alloxanthine]]
-[[Category: Covalently bound inhibitor]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Iron-sulfur]]
-[[Category: Molybdopterin]]
-[[Category: Oxipurinol]]
-[[Category: Oxypurinol]]
-[[Category: Peroxisome]]
-[[Category: Xanthine dehydrogenase]]
-[[Category: Xanthine oxidase]]
-[[Category: Xanthine oxidoreductase]]