1JXV | pdb_00001jxv

Crystal Structure of Human Nucleoside Diphosphate Kinase A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.263 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.220 (DCC) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

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: 340-342


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside Diphosphate Kinase A
A, B, C, D, E
152Homo sapiensMutation(s): 0 
Gene Names: nm23-H1
EC: 2.7.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P15531 (Homo sapiens)
Explore P15531 
Go to UniProtKB:  P15531
PHAROS:  P15531
GTEx:  ENSG00000239672 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15531
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.263 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.21α = 90
b = 78.11β = 101.33
c = 82.29γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description