1LWX

AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Structural Biology Knowledgebase: 1LWX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 1LWX

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 51650.60

Macromolecule Entities
Molecule Chains Length Organism Details
NUCLEOSIDE DIPHOSPHATE KINASE A, B, C 155 Dictyostelium discoideum EC#: 2.7.4.6 IUBMB
Mutation: N119A
Gene Name(s): ndkC-1 gip17 ndkB DDB_G0273069 ndkC-2 DDB_G0273805
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AZD
Query on AZD

A, B, C 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
QOYVAFWJURKBJG-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.216
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.59 α = 90.00
b = 71.59 β = 90.00
c = 152.70 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-04-30
  • Released Date: 1997-08-20
  • Deposition author(s): Janin, J., Xu, Y.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4