1xqi: Difference between revisions

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OCA

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 ==Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum==
-<StructureSection load='1xqi' size='340' side='right' caption='[[1xqi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1xqi' size='340' side='right'caption='[[1xqi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xqi]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xqi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XQI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1npk|1npk]]</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=1xqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqi OCA], [https://pdbe.org/1xqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xqi RCSB], [https://www.ebi.ac.uk/pdbsum/1xqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqi ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1xqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqi OCA], [http://pdbe.org/1xqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xqi RCSB], [http://www.ebi.ac.uk/pdbsum/1xqi PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NDK_PYRAE NDK_PYRAE]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
+[https://www.uniprot.org/uniprot/NDK_PYRAE NDK_PYRAE] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
 == 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/xq/1xqi_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xq/1xqi_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]]
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 51768]]
+[[Category: Large Structures]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Pyrobaculum aerophilum]]
-[[Category: Berendzen, J]]
+[[Category: Berendzen J]]
-[[Category: Cabantous, S]]
+[[Category: Cabantous S]]
-[[Category: Liong, E C]]
+[[Category: Liong EC]]
-[[Category: Pedelacq, J D]]
+[[Category: Pedelacq JD]]
-[[Category: Terwilliger, T C]]
+[[Category: Terwilliger TC]]
-[[Category: Waldo, G S]]
+[[Category: Waldo GS]]
-[[Category: Alpha/beta sandwich]]
-[[Category: Ferredoxin fold]]
-[[Category: Transferase]]