2FDJ

Crystal Structure of AlkB in complex with Fe(II) and succinate

Structural Biology Knowledgebase: 2FDJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FDJ

Classification: OXIDOREDUCTASE

Total Structure Weight: 23785.09

Macromolecule Entities
Molecule Chains Length Organism Details
Alkylated DNA repair protein alkB A 211 Escherichia coli EC#: 1.14.11.33 IUBMB
Fragment: residues 12-216
Gene Name(s): alkB aidD b2212 JW2200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.178
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 36.77 α = 75.65
b = 38.71 β = 74.65
c = 40.26 γ = 66.23

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-14
  • Released Date: 2006-02-21
  • Deposition author(s): Yu, B., Benach, J., Edstrom, W.C., Gibney, B.R., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History

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