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==Crystal structure of nucleoside diphosphate kinase in complex with ATP analog== | ==Crystal structure of nucleoside diphosphate kinase in complex with ATP analog== | ||
<StructureSection load='2dxd' size='340' side='right' caption='[[2dxd]], [[Resolution|resolution]] 1.77Å' scene=''> | <StructureSection load='2dxd' size='340' side='right'caption='[[2dxd]], [[Resolution|resolution]] 1.77Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2dxd]] is a 2 chain structure with sequence from [ | <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> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77Å</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> | |||
<tr><td class="sblockLbl"><b>[[ | <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> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | == Function == | ||
<table> | [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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dx/2dxd_consurf.spt"</scriptWhenChecked> | <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> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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> | <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]] | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Pyrococcus horikoshii]] | [[Category: Pyrococcus horikoshii OT3]] | ||
[[Category: Kato-Murayama | [[Category: Kato-Murayama M]] | ||
[[Category: Murayama | [[Category: Murayama K]] | ||
[[Category: Shirouzu M]] | |||
[[Category: Shirouzu | [[Category: Terada T]] | ||
[[Category: Terada | [[Category: Yokoyama S]] | ||
[[Category: Yokoyama | |||
Latest revision as of 11:31, 25 October 2023
Crystal structure of nucleoside diphosphate kinase in complex with ATP analogCrystal structure of nucleoside diphosphate kinase in complex with ATP analog
Structural highlights
FunctionNDK_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 Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. See Also |
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