1NDC

X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION

Structural Biology Knowledgebase: 1NDC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Observed: 0.183

Literature

Macromolecules
Sequence Display for 1NDC

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 17242.98

Macromolecule Entities
Molecule Chains Length Organism Details
NUCLEOSIDE DIPHOSPHATE KINASE A 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
TYD
Query on TYD

A THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A 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: 2.0 Å
  • R-Value Observed: 0.183
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 79.80 α = 90.00
b = 79.80 β = 90.00
c = 160.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1994-04-27
  • Released Date: 1994-06-22
  • Deposition author(s): Cherfils, J., Morera, S., Janin, J.

Revision History

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