1ZS6 | pdb_00001zs6

structure of human nucleoside-diphosphate kinase 3

• PDB DOI: https://doi.org/10.2210/pdb1ZS6/pdb

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


• Deposited: 2005-05-23 Released: 2005-06-07 
• Deposition Author(s): Choe, J., Dimov, S., Arrowsmith, C., Edwards, A., Sundstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structure of human nucleoside-diphosphate kinase 3

Dimov, S., Choe, J., ARROWSMITH, C., EDWARDS, A., SUNDSTROM, M., BOCHKAREV, A., PARK, H.

To be published.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 58.4 kDa 
• Atom Count: 3,773 
• Modeled Residue Count: 456 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase 3	A, B, C [auth D]	169	Homo sapiens	Mutation(s): 0  Gene Names: NME3 EC: 2.7.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q13232 (Homo sapiens) Explore Q13232  Go to UniProtKB:  Q13232
PHAROS:  Q13232 GTEx:  ENSG00000103024

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], E [auth B], F [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.614	α = 90
b = 86.614	β = 90
c = 126.856	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Choe, J., Dimov, S., Arrowsmith, C., Edwards, A., Sundstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description