2dy9

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[[Image:2dy9.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of nucleoside diphosphate kinase in complex with ADP==
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|PDB= 2dy9 |SIZE=350|CAPTION= <scene name='initialview01'>2dy9</scene>, resolution 2.01&Aring;
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<StructureSection load='2dy9' size='340' side='right'caption='[[2dy9]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>
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<table><tr><td colspan='2'>[[2dy9]] 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=2DY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DY9 FirstGlance]. <br>
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|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]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
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|GENE= ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy9 OCA], [https://pdbe.org/2dy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dy9 RCSB], [https://www.ebi.ac.uk/pdbsum/2dy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy9 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dy9 TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dy9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2dy9 ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of nucleoside diphosphate kinase in complex with ADP'''
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==See Also==
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*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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__TOC__
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==About this Structure==
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</StructureSection>
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2DY9 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=2DY9 OCA].
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[[Category: Large Structures]]
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: Pyrococcus horikoshii]]
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[[Category: Kato-Murayama M]]
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[[Category: Single protein]]
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[[Category: Murayama K]]
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[[Category: Kato-Murayama, M.]]
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[[Category: Shirouzu M]]
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[[Category: Murayama, K.]]
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[[Category: Terada T]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama S]]
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[[Category: Shirouzu, M.]]
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[[Category: Terada, T.]]
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[[Category: Yokoyama, S.]]
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[[Category: ADP]]
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[[Category: CL]]
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[[Category: MG]]
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[[Category: kinase]]
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[[Category: national project on protein structural and functional analyse]]
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[[Category: nppsfa]]
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[[Category: nucleoside binding]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:33:06 2008''
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Current revision

Crystal structure of nucleoside diphosphate kinase in complex with ADP

PDB ID 2dy9

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