2dy9
From Proteopedia
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| - | [[Image:2dy9.png|left|200px]] | ||
| - | + | ==Crystal structure of nucleoside diphosphate kinase in complex with ADP== | |
| - | + | <StructureSection load='2dy9' size='340' side='right'caption='[[2dy9]], [[Resolution|resolution]] 2.01Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <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> | |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01Å</td></tr> | |
| - | == | + | <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> |
| - | [[2dy9]] is a 2 chain structure with sequence from [ | + | <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> |
| + | </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/dy/2dy9_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=2dy9 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]] | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| - | [[Category: | + | __TOC__ |
| - | [[Category: Pyrococcus horikoshii]] | + | </StructureSection> |
| - | [[Category: Kato-Murayama | + | [[Category: Large Structures]] |
| - | [[Category: Murayama | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | + | [[Category: Kato-Murayama M]] | |
| - | [[Category: Shirouzu | + | [[Category: Murayama K]] |
| - | [[Category: Terada | + | [[Category: Shirouzu M]] |
| - | [[Category: Yokoyama | + | [[Category: Terada T]] |
| - | + | [[Category: Yokoyama S]] | |
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Current revision
Crystal structure of nucleoside diphosphate kinase in complex with ADP
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