3BKZ

X-ray structure of E coli AlkB crosslinked to dsDNA in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 3BKZ

Classification: DNA REPAIR OXIDOREDUCTASE / DNA

Total Structure Weight: 30472.93


Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-ketoglutarate-dependent dioxygenase alkB A 201 Escherichia coli EC#: 1.14.11.33 IUBMB
Mutation: D135C
Gene Name(s): alkB aidD b2212 JW2200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3') B 13 synthetic
DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3') C 13 synthetic

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

A 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
2YR
Query on 2YR
B NON-POLYMER C11 H18 N3 O7 P S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.188
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 41.40 α = 90.00
b = 75.51 β = 105.45
c = 46.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-09
  • Released Date: 2008-04-22
  • Deposition author(s): Yi, C., Yang, C.-G., He, C.

Revision History

  • 2011-07-13
    Type: Advisory, Version format compliance
  • 2014-05-28
    Type: Non-polymer description, Structure summary