2dxd: Difference between revisions

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-[[Image:2dxd.jpg|left|200px]]
- {{Structure
+==Crystal structure of nucleoside diphosphate kinase in complex with ATP analog==
-|PDB= 2dxd |SIZE=350|CAPTION= <scene name='initialview01'>2dxd</scene>, resolution 1.77&Aring;
+<StructureSection load='2dxd' size='340' side='right'caption='[[2dxd]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER'>ANP</scene>
+<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>
-|ACTIVITY= [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]
+</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>
-|GENE= ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])
+<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>
-}}
+<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 [[Single protein]] structure of sequence 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: Single protein]]
+[[Category: Murayama K]]
-[[Category: Kato-Murayama, M.]]
+[[Category: Shirouzu M]]
-[[Category: Murayama, K.]]
+[[Category: Terada T]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Yokoyama S]]
-[[Category: Shirouzu, M.]]
-[[Category: Terada, T.]]
-[[Category: Yokoyama, S.]]
-[[Category: ANP]]
-[[Category: CL]]
-[[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 Thu Mar 20 16:32:47 2008''