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 

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

  • 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 aggre ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside diphosphate kinase A
A, B, C
152Homo sapiensGene Names: NME1 (NDPKA, NM23)
EC: 2.7.4.6
Find proteins for P15531 (Homo sapiens)
Go to Gene View: NME1
Go to UniProtKB:  P15531
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download 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 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.260α = 90.00
b = 114.260β = 90.00
c = 89.789γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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