1F6T

STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX

Structural Biology Knowledgebase: 1F6T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 1F6T

Classification: TRANSFERASE

Total Structure Weight: 51722.45

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE) A, B, C 155 Dictyostelium discoideum EC#: 2.7.4.6 IUBMB
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
TBD
Query on TBD

A, B, C 2*-DEOXY-THYMIDINE-5*-ALPHA BORANO DIPHOSPHATE (ISOMER RP)
C10 H19 B N2 O10 P2
QDZZFSSDQOLCBV-TYNZIUOXSA-N
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.228
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.36 α = 90.00
b = 70.36 β = 90.00
c = 153.79 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-06-23
  • Released Date: 2000-09-13
  • Deposition author(s): Guerreiro, C., Boretto, J., Janin, J., Veron, M., Canard, B., Schneider, B., Sarfati, S., Deville-Bonne, D.

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