2dxd: Difference between revisions

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-[[Image:2dxd.jpg|left|200px]]<br /><applet load="2dxd" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2dxd, resolution 1.77&Aring;" />
-'''Crystal structure of nucleoside diphosphate kinase in complex with ATP analog'''<br />
-==About this Structure==
+==Crystal structure of nucleoside diphosphate kinase in complex with ATP analog==
-DXD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=ANP:'>ANP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXD OCA].
+<StructureSection load='2dxd' size='340' side='right'caption='[[2dxd]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
-[[Category: Nucleoside-diphosphate kinase]]
+== Structural highlights ==
-[[Category: Pyrococcus horikoshii]]
+<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>
-[[Category: Single protein]]
+</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>
-[[Category: Kato-Murayama, M.]]
+<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>
-[[Category: Murayama, K.]]
+<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>
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+</table>
-[[Category: Shirouzu, M.]]
+== Function ==
-[[Category: Terada, T.]]
+[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.
-[[Category: Yokoyama, S.]]
+== Evolutionary Conservation ==
-[[Category: ANP]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: CL]]
+Check<jmol>
-[[Category: kinase]]
+  <jmolCheckbox>
-[[Category: national project on protein structural and functional analyses]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dx/2dxd_consurf.spt"</scriptWhenChecked>
-[[Category: nppsfa]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: nucleoside binding]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: riken structural genomics/proteomics initiative]]
+  </jmolCheckbox>
-[[Category: rsgi]]
+</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].
-[[Category: structural genomics]]
+<div style="clear:both"></div>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:03:43 2008''
+==See Also==
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pyrococcus horikoshii OT3]]
+[[Category: Kato-Murayama M]]
+[[Category: Murayama K]]
+[[Category: Shirouzu M]]
+[[Category: Terada T]]
+[[Category: Yokoyama S]]