Macromolecule Content

Total Structure Weight: 108.08 kDa
Atom Count: 7,295
Modelled Residue Count: 928
Deposited Residue Count: 954
Unique protein chains: 1

7Z3Y

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545

PDB DOI: https://doi.org/10.2210/pdb7Z3Y/pdb

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

Deposited: 2022-03-02 Released: 2023-03-22
Deposition Author(s): Scaletti, E.R., Stenmark, P.
Funding Organization(s): Cancerfonden

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.310
R-Value Work: 0.260

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH013545

Scaletti, E.R., Stenmark, P.

To be published.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A [auth AAA], B [auth BBB], C [auth CCC]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O08760
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I9U (Subject of Investigation/LOI) Query on I9U Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA]	D [auth AAA]	2-[4-(3,5-dimethylpyrazol-1-yl)-2,6-bis(fluoranyl)phenyl]-~{N}-(4,5,6,7-tetrahydro-1,2-benzoxazol-3-yl)ethanamide C₂₀ H₂₀ F₂ N₄ O₂ KHMWCMCBIAGTAK-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain G [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain G [auth BBB]	E [auth AAA], G [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA]	F [auth AAA]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.310
R-Value Work: 0.260
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.995	α = 90
b = 81.831	β = 90
c = 168.952	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancerfonden	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.