2pgl: Difference between revisions

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 ==Catalysis associated conformational changes revealed by human CD38 complexed with a non-hydrolyzable substrate analog==
-<StructureSection load='2pgl' size='340' side='right' caption='[[2pgl]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
+<StructureSection load='2pgl' size='340' side='right'caption='[[2pgl]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pgl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pgl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N1C:N1-CYCLIC+INOSINE+5-DIPHOSPHORIBOSE'>N1C</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]] 1.76&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2pgj|2pgj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N1C:N1-CYCLIC+INOSINE+5-DIPHOSPHORIBOSE'>N1C</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CD38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2pgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgl OCA], [https://pdbe.org/2pgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgl RCSB], [https://www.ebi.ac.uk/pdbsum/2pgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgl 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/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=2pgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgl OCA], [http://pdbe.org/2pgl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgl RCSB], [http://www.ebi.ac.uk/pdbsum/2pgl PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
+[https://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
 == 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/pg/2pgl_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgl_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>
-</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=2pgl ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Graeff, R]]
+[[Category: Large Structures]]
-[[Category: Hao, Q]]
+[[Category: Graeff R]]
-[[Category: Kriksunov, I A]]
+[[Category: Hao Q]]
-[[Category: Lee, H C]]
+[[Category: Kriksunov IA]]
-[[Category: Liu, Q]]
+[[Category: Lee HC]]
-[[Category: Moreau, C]]
+[[Category: Liu Q]]
-[[Category: Potter, B V.L]]
+[[Category: Moreau C]]
-[[Category: Conformational changes of the active site]]
+[[Category: Potter BVL]]
-[[Category: Human cd38 e226q mutant bound with n1-cidpr]]
-[[Category: Hydrolase]]
-[[Category: Substrate analog binding]]
-[[Category: The catalytic pocket]]