2dxd: Difference between revisions

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-{{Seed}}
-[[Image:2dxd.png|left|200px]]
-<!--
+==Crystal structure of nucleoside diphosphate kinase in complex with ATP analog==
-The line below this paragraph, containing "STRUCTURE_2dxd", creates the "Structure Box" on the page.
+<StructureSection load='2dxd' size='340' side='right'caption='[[2dxd]], [[Resolution|resolution]] 1.77&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'>[[2dxd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXD 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]] 1.77&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-{{STRUCTURE_2dxd|  PDB=2dxd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxd OCA], [https://pdbe.org/2dxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxd RCSB], [https://www.ebi.ac.uk/pdbsum/2dxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxd ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxd TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDK_PYRHO NDK_PYRHO] 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.
+== 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/dx/2dxd_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=2dxd ConSurf].
+<div style="clear:both"></div>
-===Crystal structure of nucleoside diphosphate kinase in complex with ATP analog===
+==See Also==
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
+__TOC__
-==About this Structure==
+</StructureSection>
-DXD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXD OCA].
+[[Category: Large Structures]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Kato-Murayama M]]
-[[Category: Kato-Murayama, M.]]
+[[Category: Murayama K]]
-[[Category: Murayama, K.]]
+[[Category: Shirouzu M]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Terada T]]
-[[Category: Shirouzu, M.]]
+[[Category: Yokoyama S]]
-[[Category: Terada, T.]]
-[[Category: Yokoyama, S.]]
-[[Category: Kinase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Nucleoside binding]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 11:06:17 2008''