1KDN

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE

Structural Biology Knowledgebase: 1KDN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 1KDN

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 52055.91

Macromolecule Entities
Molecule Chains Length Organism Details
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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B, C ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AF3
Query on AF3

A, B, C ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.177
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.35 α = 90.00
b = 71.35 β = 90.00
c = 153.49 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-09-10
  • Released Date: 1997-04-21
  • Deposition author(s): Cherfils, J., Xu, Y.W., Morera, S., Janin, J.

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