2FD8

Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T

Structural Biology Knowledgebase: 2FD8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FD8

Classification: OXIDOREDUCTASE / DNA

Total Structure Weight: 24704.82


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
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*TP*(MA7)P*T)-3' B 3 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
 
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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MA7
Query on MA7
B DNA LINKING C11 H17 N5 O6 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186
  • Space Group: P 43
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.75 α = 90.00
b = 40.75 β = 90.00
c = 118.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-13
  • 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
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update