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1lwy

hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine

Method: X-RAY DIFFRACTION Dmax: 74.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

8-OXOGUANINE DNA GLYCOSYLASE

Homo sapiens

UniProt O15527

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 12–327 Fragment：CORE FRAGMENT (RESIDUES 12 TO 327) 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' × 1 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*TP*AP*CP*C)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；sodium cacodylate, calcium acetate, PEG 8000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.01 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1LWY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EBM CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE Deposited 2000-01-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa） Fragment：CORE FRAGMENT (RESIDUES 12 TO 325)
Mutation：K249Q CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, sodium cacodylate, calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.263
1FN7 COUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCISION DNA REPAIR PROTEIN Deposited 2000-08-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 16-18% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.270
1HU0 CRYSTAL STRUCTURE OF AN HOGG1-DNA BOROHYDRIDE TRAPPED INTERMEDIATE COMPLEX Deposited 2001-01-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：CORE FRAGMENT (RESIDUES 12 TO 327)
Not recorded CA CALCIUM ION × 1 OXG 8-OXOGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, calcium acetate, sodium cacodylate, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.35 Å R-free 0.245
1KO9 Native Structure of the Human 8-oxoguanine DNA Glycosylase hOGG1 Deposited 2001-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 4.6；277 K；PEG 4000, Ammonium Sulphate, Sodium citrate, pH 4.6, Microbatch, temperature 277K
Resolution 2.15 Å R-free 0.252
1LWV Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine Deposited 2002-06-03 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：CORE FRAGMENT (RESIDUES 12-327)
Not recorded CA CALCIUM ION × 1 ANG 8-AMINOGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；sodium cacodylate, calcium acetate, PEG 8000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.269
1LWW Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-bromoguanine Deposited 2002-06-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：CORE FRAGMENT (RESIDUES 12 TO 327)
Not recorded CA CALCIUM ION × 1 BRG 8-BROMOGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；sodium cacodylate, calcium acetate, PEG 8000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.257
1M3H Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide Deposited 2002-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 12–325（314 aa） Fragment：core fragment (residues 12-325)
Mutation：D268E CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, cacodylate, Calcium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.282
1M3Q Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine Deposited 2002-06-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa） Fragment：core fragment (residues 12-325)
Mutation：d268e CA CALCIUM ION × 1 ANG 8-AMINOGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.268
1N39 Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase Deposited 2002-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa）
Mutation：D268E CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16-18% PEG 8000, 200mM Ca(OAC)2, 100mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.273
1N3A Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase Deposited 2002-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa）
Mutation：D268Q CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；cacodylate, calcium acetate, 16-18% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.262
1N3C Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase Deposited 2002-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa） Fragment：3.2.2.-, 4.2.99.18
Mutation：D268N CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；sodium cacodylate, calcium acetate, PEG 8000 (16-18%), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.273
1YQK Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA Deposited 2005-02-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase
Mutation：N149C CA CALCIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.270
1YQL Catalytically inactive hOGG1 crosslinked with 7-deaza-8-azaguanine containing DNA Deposited 2005-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase
Mutation：N149C,K249Q CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.260
1YQM Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA Deposited 2005-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase
Mutation：N149C,K249Q CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.261
1YQR Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA Deposited 2005-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-OXOGUANINE DNA GLYCOSYLASE
Mutation：N149C,K249Q CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.43 Å R-free 0.251
2I5W Structure of hOGG1 crosslinked to DNA sampling a normal G adjacent to an oxoG Deposited 2006-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–323（312 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase, AP lyase
Mutation：N149C CA CALCIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；16-18% PEG 8000, 150 mM CaCl2, 100 mM sod. cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.266
2NOB Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA Deposited 2006-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：N149C,K249Q,H270A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, Ca(OAc)2, Na cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Resolution 2.10 Å R-free 0.258
2NOE Structure of catalytically inactive G42A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA Deposited 2006-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：G42A,K249Q CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, Ca(OAc)2, Na cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Resolution 2.20 Å R-free 0.269
2NOF Structure of Q315F human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA Deposited 2006-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：N149C,Q315F CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 8000, CaCl2, Na cacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 277K
Resolution 2.35 Å R-free 0.270
2NOH Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA Deposited 2006-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：K249Q,Q315A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 8000, Ca(OAc)2, Na cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Resolution 2.01 Å R-free 0.242
2NOI Structure of G42A human 8-oxoguanine glycosylase crosslinked to undamaged G-containing DNA Deposited 2006-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：G42A,N149C,K249Q CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 8000, CaCl2, Na cacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 277K
Resolution 2.35 Å R-free 0.259
2NOL Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxoG DNA Deposited 2006-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：K249Q,S292C CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 8000, CaCl2, Na cacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 277K
Resolution 2.57 Å R-free 0.250
2NOZ Structure of Q315F human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA Deposited 2006-10-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–327（316 aa） Fragment：8-oxoguanine DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase
Mutation：S292C,Q315F CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 8000, CaCl2, Na cacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.43 Å R-free 0.275
2XHI Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase Deposited 2010-06-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–345（345 aa）
Mutation：YES CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å R-free 0.265
3IH7 Crystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA Deposited 2009-07-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa） Fragment：UNP residues 12-325
Mutation：S292C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；63 mM Magnesium acetate, 12.6% PEG 8000, 90 mM Sodium cacodylate, 10 mM Sodium acetate pH 4.6, 60 mM Sodium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.10 Å R-free 0.267
3KTU Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA Deposited 2009-11-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa） Fragment：sequence database residues 12-325
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；277 K；Calcium Chloride, Sodium Cacodylate, pH 6.0, PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.257
5AN4 Crystal structure of the human 8-oxoguanine glycosylase (OGG1) processed with the CrystalDirect automated mounting and cryo-cooling technology Deposited 2015-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 12–323（312 aa） Fragment：UNP RESIDUES 12-323
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M SODIUM CITRATE, PH=5.5, 0.2 M AMMONIUM SULFATE, 24 % PEG 3350
Resolution 1.60 Å R-free 0.214
6RLW Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487 Deposited 2019-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 11–327（317 aa）
Not recorded K8Q 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Resolution 2.00 Å R-free 0.274
6RLW Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487 Deposited 2019-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 11–327（317 aa）
Not recorded K8Q 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Resolution 2.00 Å R-free 0.274
6RLW Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487 Deposited 2019-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain CCC 11–327（317 aa）
Not recorded K8Q 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Resolution 2.00 Å R-free 0.274
6RLW Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487 Deposited 2019-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain DDD 11–327（317 aa）
Not recorded K8Q 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Resolution 2.00 Å R-free 0.274
6RLW Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487 Deposited 2019-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain EEE 11–327（317 aa）
Not recorded K8Q 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Resolution 2.00 Å R-free 0.274
6W0M Human 8-oxoguanine glycosylase crosslinked with oxoG lesion containing DNA Deposited 2020-03-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa）
Mutation：E122Q, Y207C, K249Q MG MAGNESIUM ION × 2 S5Y 2-(2-ethoxyethoxy)ethanethiol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100 mM sodium cacodylate, pH 6.5, 200 mM MgCl2, and 18 % polyethylene glycol 8000.
Resolution 2.37 Å R-free 0.266
6W0R Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA Deposited 2020-03-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–323（312 aa）
Mutation：E122Q, Y207C NA SODIUM ION × 1 NO3 NITRATE ION × 3 S5Y 2-(2-ethoxyethoxy)ethanethiol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；200 mM NH4NO3, and 20 % polyethylene glycol 3350
Resolution 2.35 Å R-free 0.249
6W13 Human 8-oxoguanine glycosylase interrogating fully intrahelical oxoG lesion DNA Deposited 2020-03-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–325（314 aa）
Mutation：E122Q, Y207C, C253W MG MAGNESIUM ION × 4 ACT ACETATE ION × 2 S5Y 2-(2-ethoxyethoxy)ethanethiol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium cacodylate, pH 6.1, 200 mM MgOAc, and 17 % polyethylene glycol 8000
Resolution 2.38 Å R-free 0.271
7AYY Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785 Deposited 2020-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 11–327（317 aa）
Not recorded SEQ ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Resolution 2.00 Å R-free 0.250
7AYY Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785 Deposited 2020-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 11–327（317 aa）
Not recorded SEQ ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Resolution 2.00 Å R-free 0.250
7AYY Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785 Deposited 2020-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain CCC 11–327（317 aa）
Not recorded SEQ ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Resolution 2.00 Å R-free 0.250
7AYY Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785 Deposited 2020-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain DDD 11–327（317 aa）
Not recorded SEQ ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Resolution 2.00 Å R-free 0.250
7AYY Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785 Deposited 2020-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain EEE 11–327（317 aa）
Not recorded SEQ ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Resolution 2.00 Å R-free 0.250
8VWT OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–345（345 aa）
Mutation：Q249K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VWV OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Deposited 2024-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–345（345 aa）
Mutation：Q249K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8VX4 Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle Deposited 2024-02-03 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 2–345（344 aa）
Mutation：K249Q No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 2–345（344 aa）
Mutation：K249Q No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XWC Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the substrate 8-oxoguanine DNA at pH 8.0 under 277 K Deposited 2024-01-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 12–345（334 aa）
Mutation：K249H PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Sodium cacodylate, MgCl2, PEG 4000, glycerol
Resolution 1.45 Å R-free 0.179
8XWU Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 277 K for 24 hourss Deposited 2024-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 12–345（334 aa）
Not recorded A1LXK [(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] dihydrogen phosphate × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；sodium cacodylate, PEG 4000, MgCl2
Resolution 1.68 Å R-free 0.213
8XXG Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 277 K for 2.5 hours Deposited 2024-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 12–345（334 aa）
Mutation：K249H A1LXK [(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] dihydrogen phosphate × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；PEG 4000, MgCl2, Sodium cacodylate, glycerol
Resolution 1.82 Å R-free 0.194
8XXK Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 298 K for 3 weeks Deposited 2024-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 12–345（334 aa）
Not recorded A1LXK [(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] dihydrogen phosphate × 1 GOL GLYCEROL × 4 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；MgCl2, PEG 4000, Sodium Cacodylate, glycerol
Resolution 1.70 Å R-free 0.213
9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–345（344 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9KKY Co-crystal structure of human 8-oxoguanine glycosylase N149C mutant with DNA containing photocaged 8-oxoguanine Deposited 2024-11-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 11–327（317 aa）
Not recorded CA CALCIUM ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 6000, calcium chloride, sodium cacodylate
Resolution 2.81 Å R-free 0.262
9KL8 Co-crystal structure of human 8-oxoguanine glycosylase N149C mutant with DNA containing photocaged 8-oxoguanine after deprotection Deposited 2024-11-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 11–327（317 aa）
Mutation：N149C CA CALCIUM ION × 9 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 6000, calcium chloride, sodium cacodylate
Resolution 2.48 Å R-free 0.251
9NZ8 Crystal structure of human OGG1 in a DNA-free state Deposited 2025-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 12–327（316 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；288 K；100 mM sodium citrate, pH 5.0, 22% PEG6000, 5% ammonium sulfate (saturated)
Resolution 1.85 Å R-free 0.199
9NZ9 Crystal structure of product-bound human OGG1(WT) Deposited 2025-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 12–327（316 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；50 mM MES, pH 6.0, 16-23% PEG6000, cryoprotectant: 25% ethylene glycol
Resolution 2.00 Å R-free 0.242
9NZA Crystal structure of human OGG1 (WT) in a product bound state in the presence of the agonist F01 Deposited 2025-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 12–327（316 aa）
Not recorded OXG 8-OXOGUANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；50 mM MES, pH 6.0, 16-23% PEG6000, 4.5 mM F01, cryoprotectant: 25% ethylene glycol
Resolution 2.50 Å R-free 0.246

46 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OGG1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 9–324； UniProt 12–327

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1lwy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1lwy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1lwy
Deposition date deposition_date2002-06-03
Structure title titlehOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine
Keywords keywords;DNA REPAIR, DNA GLYCOSYLASE, PROTEIN/DNA, BOROHYDRIDE, COVALENT TRAPPING, PRODUCT-ASSISTED CATALYSIS, REACTION INTERMEDIATE, HYDROLASE-DNA COMPLEX ;; HYDROLASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.76 Å
Radius of gyration Rg (electron density) rg_electron21.43 Å
Forward intensity I(0) i042454600.00
Molecular weight molecular_weight44095.0 kDa
Excluded volume excluded_volume52414 ų
Envelope volume envelope_volume63649 ų
Hydration-shell volume shell_volume24586 ų
Envelope diameter envelope_diameter75.5 Å
Shell Rg shell_rg28.57 Å
Envelope Rg envelope_rg21.65 Å
Shape Rg shape_rg21.40 Å
Total Rg total_rg22.28 Å
Total atoms total_atoms3074
Residues n_residues343
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax74.0 Å
Rg (real space) rg_real22.65 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real4.2450e+07
I(0) uncertainty (real space) i0_real_error4.5460e+05
Rg (reciprocal space) rg_reciprocal22.68 Å
I(0) (reciprocal space) i0_reciprocal42460000.0000
Solution quality estimate total_estimate0.8913
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1 Å
Skewness Skewness skewness0.189
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5685000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1lwya1
Class classa — All alpha proteins
Fold Fold folda.96 — DNA-glycosylase
Superfamily Superfamily superfamilya.96.1 — DNA-glycosylase
Family Family familya.96.1.3 — DNA repair glycosylase, 2 C-terminal domains
Domain ID domain_idd1lwya2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.2 — DNA repair glycosylase, N-terminal domain
Domain ID domain_idd1lwya3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id1lwyA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1lwyA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id1lwyA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
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8. Citations (1)

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9. Files and Curves (10)