Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 53.28 kDa 
• Atom Count: 4030 
• Residue Count: 453 
• Unique protein chains: 1

1UCN

X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution

• DOI: 10.2210/pdb1UCN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-04-16 Released: 2003-09-30 
• Deposition Author(s): Chen, Y., Gallois-Montbrun, S., Schneider, B., Veron, M., Morera, S., Deville-Bonne, D., Janin, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.237 

Literature

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., Veron, M., Morera, S., Deville-Bonne, D., Janin, J.

(2003) J Mol Biol 332: 915-926

• PubMed: 12972261 
• DOI: 10.1016/j.jmb.2003.07.004
• Structures With Same Primary Citation


• PubMed Abstract: 
  

NDPK-A, product of the nm23-H1 gene, is one of the two major isoforms of human nucleoside diphosphate kinase. We analyzed the binding of its nucleotide substrates by fluorometric methods. The binding of nucleoside triphosphate (NTP) substrates was detected by following changes of the intrinsic fluorescence of the H118G/F60W variant, a mutant protein engineered for that purpose. Nucleoside diphosphate (NDP) substrate binding was measured by competition with a fluorescent derivative of ADP, following the fluorescence anisotropy of the derivative. We also determined an X-ray structure at 2.0A resolution of the variant NDPK-A in complex with ADP, Ca(2+) and inorganic phosphate, products of ATP hydrolysis. We compared the conformation of the bound nucleotide seen in this complex and the interactions it makes with the protein, with those of the nucleotide substrates, substrate analogues or inhibitors present in other NDP kinase structures. We also compared NDP kinase-bound nucleotides to ATP bound to protein kinases, and showed that the nucleoside monophosphate moieties have nearly identical conformations in spite of the very different protein environments. However, the beta and gamma-phosphate groups are differently positioned and oriented in the two types of kinases, and they bind metal ions with opposite chiralities. Thus, it should be possible to design nucleotide analogues that are good substrates of one type of kinase, and poor substrates or inhibitors of the other kind.

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR 9063, 91198 Gif-sur Yvette, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
nucleoside diphosphate kinase A	A, B, C	152	Homo sapiens	Mutation(s): 2  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B, C	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
TRS	B	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	A, B, C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADP	Kd:  6000   nM  Binding MOAD
ADP	Kd :  6000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.237 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.075	α = 90
b = 116.075	β = 90
c = 91.292	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-16 
• Released Date: 2003-09-30 
Deposition Author(s): Chen, Y., Gallois-Montbrun, S., Schneider, B., Veron, M., Morera, S., Deville-Bonne, D., Janin, J.

Revision History 

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance