2HVD

Human nucleoside diphosphate kinase A complexed with ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structures of S120G Mutant and Wild Type of Human Nucleoside Diphosphate Kinase A in Complex with ADP

Giraud, M.-F., Georgescauld, F., Lascu, I., Dautant, A.

(2006) J Bioenerg Biomembr 38: 261-264

  • DOI: 10.1007/s10863-006-9043-0
  • Primary Citation of Related Structures:  
    2HVE, 2HVD

  • PubMed Abstract: 

    • Nm23 was the first metastasis suppressor gene identified. This gene encodes a NDP kinase that also exhibits other properties like histidine protein kinase and interactions with proteins and DNA. The S120G mutant of NDPK-A has been identified in aggressive neuroblastomas and has been found to reduce the metastasis suppressor effect of Nm23 ...

    Nm23 was the first metastasis suppressor gene identified. This gene encodes a NDP kinase that also exhibits other properties like histidine protein kinase and interactions with proteins and DNA. The S120G mutant of NDPK-A has been identified in aggressive neuroblastomas and has been found to reduce the metastasis suppressor effect of Nm23. In order to understand the differences between the wild type and the S120G mutant, we have determined the structure of both mutant and wild type NDPK-A in complex with ADP. Our results reveal that there are no significant changes between the two enzyme versions even in the surroundings of the catalytic histidine that is required for NDP kinase activity. This suggests that the S120G mutation may affect an other protein property than NDP kinase activity.

    Related Citations: 
    • Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor
      Min, K., Song, H.K., Chang, C., Kim, S.Y., Lee, K.J., Suh, S.W.
      (2002) Proteins 46: 340
    • Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
      Chen, Y., Gallois-Montbrun, S., Schneider, B., Deville-Bonne, D., Janin, J.
      (2003) J Mol Biol 332: 915
    Organizational Affiliation: 

    Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS-Université Victor Segalen Bordeaux 2, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase A A, B, C152Homo sapiensMutation(s): 0 
Gene Names: NME1, NDPKA, NM23
EC: 2.7.4.6
Find proteins for P15531 (Homo sapiens)
Explore P15531 
Go to UniProtKB:  P15531
NIH Common Fund Data Resources
PHAROS:  P15531
GTEx:  ENSG00000239672
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.26α = 90
b = 114.26β = 90
c = 89.789γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description