2nx3: Difference between revisions

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 ==Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase==
-<StructureSection load='2nx3' size='340' side='right' caption='[[2nx3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2nx3' size='340' side='right'caption='[[2nx3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nx3]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NX3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nx3]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NX3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fwn|1fwn]], [[2nwr|2nwr]], [[2nws|2nws]], [[2nx1|2nx1]], [[2nxg|2nxg]], [[2nxh|2nxh]], [[2nxi|2nxi]], [[2nxk|2nxk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</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=2nx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nx3 OCA], [https://pdbe.org/2nx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nx3 RCSB], [https://www.ebi.ac.uk/pdbsum/2nx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nx3 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/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nx3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nx3 RCSB], [http://www.ebi.ac.uk/pdbsum/2nx3 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
 == 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/nx/2nx3_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nx/2nx3_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2nx3 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2nx3" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: 3-deoxy-8-phosphooctulonate synthase]]
 [[Category: Aquifex aeolicus]]
-[[Category: Gatti, D L]]
+[[Category: Large Structures]]
-[[Category: Kona, F]]
+[[Category: Gatti DL]]
-[[Category: Kuzmic, P]]
+[[Category: Kona F]]
-[[Category: Martin, P]]
+[[Category: Kuzmic P]]
-[[Category: Xu, X]]
+[[Category: Martin P]]
-[[Category: A5p]]
+[[Category: Xu X]]
-[[Category: Kdo]]
-[[Category: Kdo8p]]
-[[Category: Pep]]
-[[Category: Transferase]]