1BUX

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Structural Biology Knowledgebase: 1BUX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.312
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 1BUX

Classification: PHOSPHOTRANSFERASE

Total Structure Weight: 51971.24

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 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PPS
Query on PPS

A, B, C 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE
C10 H15 N5 O13 P2 S
GACDQMDRPRGCTN-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PPS N/A in BindingDB
N/A in BindingMoad
Kd: 14000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.312
  • R-Value Work: 0.204
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 71.50 α = 90.00
b = 71.50 β = 90.00
c = 153.90 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-09-07
  • Released Date: 1999-04-27
  • Deposition author(s): Xu, Y., Schneider, B., Deville-Bonne, D., Veron, M., Janin, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4