9FNU | pdb_00009fnu

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13579

• PDB DOI: https://doi.org/10.2210/pdb9FNU/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-11 Released: 2025-06-25 
• Deposition Author(s): Scaletti, E., Stenmark, P.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.224 (DCC) 

Starting Model: experimental

Literature

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH13579

Scaletti, E., Stenmark, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.36 kDa 
• Atom Count: 7,622 
• Modeled Residue Count: 932 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A, B, C	318	Mus musculus	Mutation(s): 0  Gene Names: Ogg1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for O08760 (Mus musculus) Explore O08760  Go to UniProtKB:  O08760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ID3 (Subject of Investigation/LOI)	D [auth A], G [auth B], H [auth C]	3-(2-azanylethyl)-2-pyridin-3-yl-1~{H}-indol-5-ol C15 H15 N3 O CRBZVVVWGMWAMJ-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.256 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.224 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.89	α = 90
b = 81.114	β = 90
c = 170.104	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Scaletti, E., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release