2dxd: Difference between revisions

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[[Image:2dxd.png|left|200px]]


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==Crystal structure of nucleoside diphosphate kinase in complex with ATP analog==
The line below this paragraph, containing "STRUCTURE_2dxd", creates the "Structure Box" on the page.
<StructureSection load='2dxd' size='340' side='right'caption='[[2dxd]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77&#8491;</td></tr>
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<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>
{{STRUCTURE_2dxd| PDB=2dxd |  SCENE= }}
<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>
== 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/2dxd_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=2dxd ConSurf].
<div style="clear:both"></div>


===Crystal structure of nucleoside diphosphate kinase in complex with ATP analog===
==See Also==
 
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 
__TOC__
==About this Structure==
</StructureSection>
2DXD 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=2DXD 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 Sun Sep 28 17:18:47 2008''

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

2dxd 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 1.77Å
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

2dxd, resolution 1.77Å

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