3B54

Saccharomyces cerevisiae nucleoside diphosphate kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of Ynk1 from the yeast Saccharomyces cerevisiae

Wang, H.Bao, R.Jiang, C.Yang, Z.Zhou, C.-Z.Chen, Y.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 572-576

  • DOI: 10.1107/S1744309108015212
  • Primary Citation of Related Structures:  
    3B54

  • PubMed Abstract: 
  • Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of the gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. In addition to biochemical studies, a number of crystal structures of NDPK from various organisms, including both native proteins and complexes with nucleotides or nucleotide analogues, have been determined ...

    Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of the gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. In addition to biochemical studies, a number of crystal structures of NDPK from various organisms, including both native proteins and complexes with nucleotides or nucleotide analogues, have been determined. Here, the crystal structure of Ynk1, an NDPK from the yeast Saccharomyces cerevisiae, has been solved at 3.1 A resolution. Structural analysis strongly supports the oligomerization state of this protein being hexameric rather than tetrameric.


    Organizational Affiliation

    Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinaseA, B161Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NDK1YNKYNK1
EC: 2.7.4.6
Find proteins for P36010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36010 
Go to UniProtKB:  P36010
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.92α = 90
b = 185.92β = 90
c = 185.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance