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[[Image:2dxf.jpg|left|200px]]


{{Structure
==Crystal structure of nucleoside diphosphate kinase in complex with GTP analog==
|PDB= 2dxf |SIZE=350|CAPTION= <scene name='initialview01'>2dxf</scene>, resolution 1.70&Aring;
<StructureSection load='2dxf' size='340' side='right'caption='[[2dxf]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>
<table><tr><td colspan='2'>[[2dxf]] 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=2DXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXF FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[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] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxf OCA], [https://pdbe.org/2dxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxf RCSB], [https://www.ebi.ac.uk/pdbsum/2dxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxf ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxf TOPSAN]</span></td></tr>
|RELATEDENTRY=[[2dxd|2DXD]], [[2dxe|2DXE]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxf OCA], [http://www.ebi.ac.uk/pdbsum/2dxf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dxf RCSB]</span>
== 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/2dxf_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=2dxf ConSurf].
<div style="clear:both"></div>


'''Crystal structure of nucleoside diphosphate kinase in complex with GTP analog'''
==See Also==
 
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 
__TOC__
==About this Structure==
</StructureSection>
2DXF 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=2DXF 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: 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 Mon Mar 31 02:40:56 2008''

Latest revision as of 11:31, 25 October 2023

Crystal structure of nucleoside diphosphate kinase in complex with GTP analogCrystal structure of nucleoside diphosphate kinase in complex with GTP analog

Structural highlights

2dxf is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2dxf, resolution 1.70Å

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