1n39

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

Method: X-RAY DIFFRACTION D_max: 73.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

N-glycosylase/DNA lyase

Homo sapiens

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 12–325	Mutation：D268E	DNA complement strand × 1 DNA inhibitor strand × 1 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

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 1N39	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 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 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）	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 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：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 mutation/modification 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 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：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 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：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
1LWY hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine Deposited 2002-06-03	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 12–327（316 aa） Fragment：CORE FRAGMENT (RESIDUES 12 TO 327)	Not recorded	No recorded non-water small molecule	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
1M3H Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide Deposited 2002-06-27	Different construct Different oligomeric state 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
1N3A Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase Deposited 2002-10-25	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）	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 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 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 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 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：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 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：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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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）	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 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）	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 mutation/modification Different oligomeric state Different ligand/ion 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 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）	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 mutation/modification 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 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 12–327（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 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 12–327（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 4–317； UniProt 12–325

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1n39
Deposition date deposition_date	2002-10-25
Structure title title	Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase
Keywords keywords	HhH-GPD, DNA-repair, glycosylase, oxoguanine, hydrolase, lyase-DNA COMPLEX; hydrolase, lyase/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.74 Å
Radius of gyration Rg (electron density) rg_electron	21.40 Å
Forward intensity I(0) i0	41278100.00
Molecular weight molecular_weight	43609.0 kDa
Excluded volume excluded_volume	51892 Å³
Envelope volume envelope_volume	63534 Å³
Hydration-shell volume shell_volume	24565 Å³
Envelope diameter envelope_diameter	74.3 Å
Shell Rg shell_rg	28.54 Å
Envelope Rg envelope_rg	21.63 Å
Shape Rg shape_rg	21.38 Å
Total Rg total_rg	22.24 Å
Total atoms total_atoms	3039
Residues n_residues	343
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	73.4 Å
Rg (real space) rg_real	22.62 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.1280e+07
I(0) uncertainty (real space) i0_real_error	5.6620e+05
Rg (reciprocal space) rg_reciprocal	22.65 Å
I(0) (reciprocal space) i0_reciprocal	41280000.0000
Solution quality estimate total_estimate	0.8940
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	72.2 Å
Skewness Skewness skewness	0.181
Kurtosis Kurtosis kurtosis	-0.376
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5328000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA complement strand
Molecular weight formula_weight	4635.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	3192

GGTAGACCTGGACGC

Entity 2 Entity 2 polymer

Description description	DNA inhibitor strand
Molecular weight formula_weight	4396.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GCGTCCANGTCTACC

Entity 3 Entity 3 polymer

Description description	N-glycosylase/DNA lyase
Molecular weight formula_weight	35662.3 kDa
EC 编号 ec_number	3.2.2.-, 4.2.99.18
Mutation mutation	D268E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GSEGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVEVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1n39a1
Class class	a — All alpha proteins
Fold Fold fold	a.96 — DNA-glycosylase
Superfamily Superfamily superfamily	a.96.1 — DNA-glycosylase
Family Family family	a.96.1.3 — DNA repair glycosylase, 2 C-terminal domains

Domain ID domain_id	d1n39a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.2 — DNA repair glycosylase, N-terminal domain

Domain ID domain_id	d1n39a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	1n39A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1n39A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

Domain ID domain_id	1n39A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

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8. Citations (1)

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Unit-cell length a length_a	92.366 Å
Unit-cell length b length_b	92.366 Å
Unit-cell length c length_c	211.277 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	29.070 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2730

fit	/app/data/saxs_computation/n3/1n39/1n39.fit
pddf	/app/data/pr_computation/n3/1n39/1n39.pr.out
profile	/app/data/saxs_computation/n3/1n39/1n39.dat

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase

1. Protein Identity and Related Structures Protein Identity & Related Structures

N-glycosylase/DNA lyase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)