1F3F

STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 1F3F

Classification: TRANSFERASE

Total Structure Weight: 52150.24

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE) A, B, C 155 Dictyostelium discoideum EC#: 2.7.4.6 IUBMB
Mutation: H122G
Gene Name(s): ndkC-1 gip17 ndkB DDB_G0273069 ndkC-2 DDB_G0273805
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
D4T
Query on D4T

A, B, C 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE
C10 H15 N2 O13 P3
ODSQODTUNULBHF-JGVFFNPUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D4D
Query on D4D

B 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE
C10 H14 N2 O10 P2
LXCAIISEDMYORY-JGVFFNPUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
D4T N/A in BindingDB
Kd: 21300 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.203
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.02 α = 90.00
b = 70.02 β = 90.00
c = 152.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-06-02
  • Released Date: 2000-09-13
  • Deposition author(s): Meyer, P., Schneider, B., Sarfati, S., Deville-Bonne, D., Guerreiro, C., Boretto, J., Janin, J., Veron, M., Canard, B.

Revision History

  • Version 1_0: 2000-09-13

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance