1LWX

AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase.

Xu, Y.Sellam, O.Morera, S.Sarfati, S.Biondi, R.Veron, M.Janin, J.

(1997) Proc Natl Acad Sci U S A 94: 7162-7165

  • DOI: 10.1073/pnas.94.14.7162
  • Primary Citation of Related Structures:  
    1LWX

  • PubMed Abstract: 
  • To be effective as antiviral agent, AZT (3'-azido-3'-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2 ...

    To be effective as antiviral agent, AZT (3'-azido-3'-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2.3-A x-ray structure of a complex with the N119A point mutant of Dictyostelium NDP kinase. It shows that the analog binds at the same site and, except for the sugar ring pucker which is different, binds in the same way as the natural substrate thymidine diphosphate. However, the azido group that replaces the 3'OH of the deoxyribose in AZT displaces a lysine side chain involved in catalysis. Moreover, it is unable to make an internal hydrogen bond to the oxygen bridging the beta- and gamma-phosphate, which plays an important part in phosphate transfer.


    Related Citations: 
    • Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium
      Morera, S., Chiadmi, M., Lebras, G., Lascu, I., Janin, J.
      (1995) Biochemistry 34: 11062
    • Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase
      Morera, S., Lascu, I., Dumas, C., Lebras, G., Briozzo, P., Veron, M., Janin, J.
      (1994) Biochemistry 33: 459

    Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, Unité Propre de Recherche 9063, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE KINASEA, B, C155Dictyostelium discoideumMutation(s): 1 
Gene Names: ndkC-1gip17ndkBDDB_G0273069ndkC-2DDB_G0273805
EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum)
Explore P22887 
Go to UniProtKB:  P22887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22887
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZD
Query on AZD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
H [auth C]
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
QOYVAFWJURKBJG-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.59α = 90
b = 71.59β = 90
c = 152.7γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other