2dxe: Difference between revisions
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== | ==Crystal structure of nucleoside diphosphate kinase in complex with GDP== | ||
<StructureSection load='2dxe' size='340' side='right'caption='[[2dxe]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
[ | == Structural highlights == | ||
[ | <table><tr><td colspan='2'>[[2dxe]] 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=2DXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXE 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]] 1.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2dxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxe OCA], [https://pdbe.org/2dxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxe RCSB], [https://www.ebi.ac.uk/pdbsum/2dxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxe ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxe 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/2dxe_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=2dxe ConSurf]. | ||
<div style="clear:both"></div> | |||
==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]] | |||
Latest revision as of 11:31, 25 October 2023
Crystal structure of nucleoside diphosphate kinase in complex with GDPCrystal structure of nucleoside diphosphate kinase in complex with GDP
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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