1KHZ

Structure of the ADPR-ase in complex with AMPCPR and Mg

Structural Biology Knowledgebase: 1KHZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1KHZ

Classification: HYDROLASE

Total Structure Weight: 48057.66

Macromolecule Entities
Molecule Chains Length Organism Details
ADP-ribose pyrophosphatase A, B 209 Escherichia coli EC#: 3.6.1.13 IUBMB
Gene Name(s): nudF aspP yqiE yzzG b3034 JW3002
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADV
Query on ADV

B ALPHA-BETA METHYLENE ADP-RIBOSE
4, (Synonym)
C16 H25 N5 O13 P2
ZPZRETFSCSWNDT-DBXCYWGHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 2.04 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.196
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 67.10 α = 90.00
b = 67.40 β = 90.00
c = 96.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-01
  • Released Date: 2002-10-09
  • Deposition author(s): Gabelli, S.B., Bianchet, M.A., Bessman, M.J., Amzel, L.M.

Revision History

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