1JXV

Crystal Structure of Human Nucleoside Diphosphate Kinase A

• PDB DOI: https://doi.org/10.2210/pdb1JXV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-09-10 Released: 2002-04-10 
• Deposition Author(s): Min, K., Song, H.K., Chang, C., Kim, S.Y., Lee, K.J., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.207 

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

• PubMed: 11835509 
• DOI: https://doi.org/10.1002/prot.10038
• Primary Citation of Related Structures:  
  1JXV

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Organizational Affiliation: 

School of Chemistry and Molecular Engineering, Seoul National University, Seoul, Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.02 kDa 
• Atom Count: 7,295 
• Modelled Residue Count: 894 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside Diphosphate Kinase A	A, B, C, D, E, F	152	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.21	α = 90
b = 78.11	β = 101.33
c = 82.29	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-10 
Deposition Author(s): Min, K., Song, H.K., Chang, C., Kim, S.Y., Lee, K.J., Suh, S.W.

Revision History  

• 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