2F5S

Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC1

Structural Biology Knowledgebase: 2F5S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 2F5S

Classification: hydrolase / DNA

Total Structure Weight: 40593.57


Macromolecule Entities
Molecule Chains Length Organism Details
formamidopyrimidine-DNA glycosidase A 274 Geobacillus stearothermophilus EC#: 3.2.2.23 IUBMB
Mutation: E3Q, Q166C
Gene Name(s): mutM fpg
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3' B 16 synthetic
5'-D(*TP*GP*C*GP*TP*CP*CP*(8OG)P*AP*GP*TP*CP*TP*AP*CP*C)-3' C 16 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
C DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.220
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.40 α = 90.00
b = 93.37 β = 90.00
c = 103.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-26
  • Released Date: 2006-03-07
  • Deposition author(s): Banerjee, A., Santos, W.L., Verdine, G.L.

Revision History

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