1NDP

ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Observed: 0.193

Literature

Macromolecules
Sequence Display for 1NDP

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 34511.38

Macromolecule Entities
Molecule Chains Length Organism Details
NUCLEOSIDE DIPHOSPHATE KINASE A, B 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
ADP
Query on ADP

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

B 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: 2.2 Å
  • R-Value Observed: 0.193
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 73.18 α = 90.00
b = 73.18 β = 90.00
c = 158.45 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-11-29
  • Released Date: 1994-04-30
  • Deposition author(s): Janin, J., Morera, S., Dumas, C., Lascu, I., Lebras, G., Veron, M.

Revision History

  • Version 1_0: 1994-04-30

    Type: Initial release

  • Version 1_1: 2008-03-25

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance