8BQ7 | pdb_00008bq7

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH2829

PDB DOI: https://doi.org/10.2210/pdb8BQ7/pdb

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

Deposited: 2022-11-19 Released: 2023-11-29
Deposition Author(s): Scaletti, E., Stenmark, P.
Funding Organization(s): Cancerfonden

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.307 (Depositor), 0.306 (DCC)
R-Value Work:
0.255 (Depositor), 0.256 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

Hank, E.C., D’Arcy-Evans, N.D., Scaletti, E.R., Benitez-Buelga, C., Wallner, O., Ortis, F., Zhou, K., Meng, L., del Prado, A., Calvo, P., Almlof, I., Wiita, E., Nierlin, K., Kosenina, S., Kramer, A., Eddershaw, A., Kehler, M., Long, M., Jemth, A.S., Dawson, H., Stewart, J., Dickey, A., Astorga, M.E., Varga, M., Homan, E.J., Scobie, M., Knapp, S., Sastre, L., Stenmark, P., de Vega, M., Helleday, T., Michel, M.

(2025) RSC Chem Biol

DOI: https://doi.org/10.1039/D4CB00323C

Macromolecule Content

Total Structure Weight: 107.83 kDa
Atom Count: 7,047
Modeled Residue Count: 913
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O08760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R4U (Subject of Investigation/LOI) Query on R4U Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	~{N}4-cyclohexyl-2~{H}-pyrazolo[3,4-d]pyrimidine-4,6-diamine C₁₁ H₁₆ N₆ IQIULFHBHXKBGP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.307 (Depositor), 0.306 (DCC)
R-Value Work: 0.255 (Depositor), 0.256 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.733	α = 90
b = 82.095	β = 90
c = 169.487	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancerfonden	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release
Version 1.1: 2025-11-12
Changes: Database references, Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.