9dp3

APE1 N174D Product Complex with Abasic DNA

Method: X-RAY DIFFRACTION D_max: 107.8 Å Quality: GOOD

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

DNA repair nuclease/redox regulator APEX1, mitochondrial

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 3 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 43–318	Mutation：tr1-42, C138A, N174D	;DNA (5'-D(P(3DR)PCPGPAPCPGPGPAPTPCPC)-3') ; × 1 ;DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3') ; × 1 ;DNA (5'-D(GPGPAPTPCPCPGPTPCPGPGPGPCPGPCPAPTPCPAPGPC)-3') ; × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM lithium sulfate, 15-25% PEG3350	Resolution 2.10 Å R-free 0.274
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 43–318	Mutation：tr1-42, C138A, N174D	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM lithium sulfate, 15-25% PEG3350	Resolution 2.10 Å R-free 0.274

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 9DP3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BIX THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL DEOXYRIBOSE AT DNA ABASIC SITES Deposited 1998-06-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–317（287 aa）	Not recorded	SM SAMARIUM (III) ION × 4 PT PLATINUM (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.20 Å R-free 0.269
1CQG HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 STRUCTURES Deposited 1996-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 58–70（13 aa） Fragment：RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CQH HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 58–70（13 aa） Fragment：RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1DE8 HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA Deposited 1999-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 42–317（276 aa） Fragment：APE1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 5000, LITHIUM SULFATE, MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.95 Å R-free 0.312
1DE8 HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA Deposited 1999-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 42–317（276 aa） Fragment：APE1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 5000, LITHIUM SULFATE, MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.95 Å R-free 0.312
1DE9 HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION Deposited 1999-11-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 42–317（276 aa） Fragment：APE1	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MPEG 2000, LITHIUM SULFATE, MANGANESE CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.274
1DE9 HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION Deposited 1999-11-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 42–317（276 aa） Fragment：APE1	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MPEG 2000, LITHIUM SULFATE, MANGANESE CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.274
1DEW CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA Deposited 1999-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 39–317（279 aa） Fragment：APE1	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 2000, LITHIUM SULFATE, CACODYLATE BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.286
1DEW CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA Deposited 1999-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 39–317（279 aa） Fragment：APE1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 2000, LITHIUM SULFATE, CACODYLATE BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.286
1E9N A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism Deposited 2000-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa）	Not recorded	PB LEAD (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT	Resolution 2.20 Å R-free 0.252
1E9N A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism Deposited 2000-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–317（317 aa）	Not recorded	PB LEAD (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT	Resolution 2.20 Å R-free 0.252
1HD7 A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism Deposited 2000-11-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa）	Not recorded	PB LEAD (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN.	Resolution 1.95 Å R-free 0.255
2ISI Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand Deposited 2006-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa）	Not recorded	PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M hepes, 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.76 Å R-free 0.284
2ISI Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand Deposited 2006-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–317（317 aa）	Not recorded	PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M hepes, 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.76 Å R-free 0.284
2ISI Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand Deposited 2006-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–317（317 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M hepes, 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.76 Å R-free 0.284
2O3H Crystal structure of the human C65A Ape Deposited 2006-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–317（279 aa）	Mutation：C65A	SM SAMARIUM (III) ION × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；20% PEG 8000, 100 mM MES pH 6.0, 7.5 mM samarium acetate, 4% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.226
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K	Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K	Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–318（318 aa）	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K	Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–318（318 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K	Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–318（318 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K	Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–318（318 aa）	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K	Resolution 2.15 Å R-free 0.243
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 2–318（317 aa）	Not recorded	MG MAGNESIUM ION × 3 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K	Resolution 2.39 Å R-free 0.246
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 2–318（317 aa）	Not recorded	MG MAGNESIUM ION × 1 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K	Resolution 2.39 Å R-free 0.246
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain C 2–318（317 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K	Resolution 2.39 Å R-free 0.246
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 2–318（317 aa）	Not recorded	MG MAGNESIUM ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K	Resolution 2.39 Å R-free 0.246
4LND Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor Deposited 2013-07-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–318（280 aa） Fragment：UNP residues 39-318	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.92 Å R-free 0.241
4LND Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor Deposited 2013-07-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 39–318（280 aa） Fragment：UNP residues 39-318	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.92 Å R-free 0.241
4LND Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor Deposited 2013-07-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 39–318（280 aa） Fragment：UNP residues 39-318	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.92 Å R-free 0.241
4QH9 Crystal structure of Mn2+ bound human APE1 Deposited 2014-05-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–318（281 aa） Fragment：UNP residues 38-318	Mutation：C138A	EDO 1,2-ETHANEDIOL × 7 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 0.2M Sodium Chloride, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.17 Å R-free 0.256
4QHD Crystal structure of apo human APE1 Deposited 2014-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–318（281 aa） Fragment：UNP residues 38-318	Mutation：C138A	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 0.2M Sodium Chloride, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.238
4QHE Crystal structure of Mg2+ bound human APE1 Deposited 2014-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–318（281 aa）	Mutation：C138A	MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 0.2M Sodium Chlorid, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.193
5CFG C2 crystal form of APE1 with Mg2+ Deposited 2015-07-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–318（275 aa） Fragment：UNP residues 44-318	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG 8000, 0.2 M MgAc and 0.1 M Cacodylate	Resolution 1.80 Å R-free 0.204
5DFF Human APE1 product complex Deposited 2015-08-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Not recorded	MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.57 Å R-free 0.211
5DFF Human APE1 product complex Deposited 2015-08-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.57 Å R-free 0.211
5DFH Human APE1 mismatch product complex Deposited 2015-08-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg20000, 100 mM sodium citrate, 200 mM MgCl	Resolution 1.95 Å R-free 0.219
5DFH Human APE1 mismatch product complex Deposited 2015-08-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg20000, 100 mM sodium citrate, 200 mM MgCl	Resolution 1.95 Å R-free 0.219
5DFI Human APE1 phosphorothioate substrate complex Deposited 2015-08-26	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: trimeric	Chain A 43–318（276 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl	Resolution 1.63 Å R-free 0.195
5DFI Human APE1 phosphorothioate substrate complex Deposited 2015-08-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl	Resolution 1.63 Å R-free 0.195
5DFJ Human APE1 E96Q/D210N mismatch substrate complex Deposited 2015-08-26	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: trimeric	Chain A 43–318（276 aa）	Mutation：E96Q, D210N	CL CHLORIDE ION × 6 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl	Resolution 1.85 Å R-free 0.200
5DFJ Human APE1 E96Q/D210N mismatch substrate complex Deposited 2015-08-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：E96Q, D210N	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl	Resolution 1.85 Å R-free 0.200
5DG0 Human APE1 phosphorothioate substrate complex with Mn2+ Deposited 2015-08-27	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: trimeric	Chain A 43–318（276 aa） Fragment：UNP residues 43-318	Not recorded	MN MANGANESE (II) ION × 6 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg 20000, 100 mM sodium citrate, 200 mM MgCl2	Resolution 1.80 Å R-free 0.205
5DG0 Human APE1 phosphorothioate substrate complex with Mn2+ Deposited 2015-08-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa） Fragment：UNP residues 43-318	Not recorded	MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg 20000, 100 mM sodium citrate, 200 mM MgCl2	Resolution 1.80 Å R-free 0.205
5WN0 APE1 exonuclease substrate complex with a C/G match Deposited 2017-07-31	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.60 Å R-free 0.275
5WN0 APE1 exonuclease substrate complex with a C/G match Deposited 2017-07-31	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.60 Å R-free 0.275
5WN1 APE1 exonuclease product complex Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.30 Å R-free 0.270
5WN1 APE1 exonuclease product complex Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.30 Å R-free 0.270
5WN2 APE1 exonuclease substrate complex with phosphoglycolate Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Not recorded	NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 PGA 2-PHOSPHOGLYCOLIC ACID × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.29 Å R-free 0.239
5WN2 APE1 exonuclease substrate complex with phosphoglycolate Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.29 Å R-free 0.239
5WN3 APE1 F266A exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：C138A, F266A	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.00 Å R-free 0.258
5WN3 APE1 F266A exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Mutation：C138A, F266A	EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.00 Å R-free 0.258
5WN4 APE1 exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Not recorded	NA SODIUM ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.10 Å R-free 0.249
5WN4 APE1 exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Not recorded	NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.10 Å R-free 0.249
5WN5 APE1 exonuclease substrate complex with a C/T mismatch and Mn2+ Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Not recorded	MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.20 Å R-free 0.261
5WN5 APE1 exonuclease substrate complex with a C/T mismatch and Mn2+ Deposited 2017-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Not recorded	MN MANGANESE (II) ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.20 Å R-free 0.261
6BOQ Human APE1 substrate complex with an A/A mismatch adjacent the THF Deposited 2017-11-20	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: trimeric	Chain A 1–318（318 aa）	Mutation：C138A	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.96 Å R-free 0.258
6BOQ Human APE1 substrate complex with an A/A mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：C138A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.96 Å R-free 0.258
6BOR Human APE1 substrate complex with an G/G mismatch adjacent the THF Deposited 2017-11-20	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: trimeric	Chain A 1–318（318 aa）	Mutation：E96Q, D210N	EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.84 Å R-free 0.209
6BOR Human APE1 substrate complex with an G/G mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：E96Q, D210N	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.84 Å R-free 0.209
6BOS Human APE1 substrate complex with an A/C mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–318（318 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 2.30 Å R-free 0.236
6BOS Human APE1 substrate complex with an A/C mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 2.30 Å R-free 0.236
6BOT Human APE1 substrate complex with an C/C mismatch adjacent the THF Deposited 2017-11-20	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: trimeric	Chain A 1–318（318 aa）	Mutation：C138A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 2.30 Å R-free 0.245
6BOT Human APE1 substrate complex with an C/C mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 2.30 Å R-free 0.245
6BOU Human APE1 substrate complex with an T/C mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–318（318 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 2.54 Å R-free 0.268
6BOU Human APE1 substrate complex with an T/C mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 2.54 Å R-free 0.268
6BOV Human APE1 substrate complex with an A/G mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–318（318 aa）	Mutation：E96Q, D210N, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.98 Å R-free 0.242
6BOV Human APE1 substrate complex with an A/G mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：E96Q, D210N, C138A	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.98 Å R-free 0.242
6BOW Human APE1 substrate complex with an T/T mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–318（318 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.59 Å R-free 0.241
6BOW Human APE1 substrate complex with an T/T mismatch adjacent the THF Deposited 2017-11-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2	Resolution 1.59 Å R-free 0.241
6MK3 Crystallographic solvent mapping analysis of DMSO bound to APE1 Deposited 2018-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–318（279 aa） Fragment：UNP residues 40-318	Not recorded	DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000	Resolution 1.48 Å R-free 0.219
6MKK Crystallographic solvent mapping analysis of DMSO/Mg bound to APE1 Deposited 2018-09-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–318（279 aa） Fragment：UNP residues 40-318	Not recorded	MG MAGNESIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000	Resolution 1.44 Å R-free 0.212
6MKM Crystallographic solvent mapping analysis of DMSO/Tris bound to APE1 Deposited 2018-09-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–318（279 aa） Fragment：UNP residues 40-318	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000	Resolution 1.67 Å R-free 0.250
6MKO Crystallographic solvent mapping analysis of glycerol bound to APE1 Deposited 2018-09-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–318（279 aa） Fragment：UNP residues 40-318	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000	Resolution 2.09 Å R-free 0.228
6P93 Human APE1 K98A AP-endonuclease product complex Deposited 2019-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric	Chain A 43–318（276 aa） Chain B 43–318（276 aa）	Mutation：K98A Mutation：K98A	MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 2.10 Å R-free 0.226
6P94 Human APE1 C65A AP-endonuclease product complex Deposited 2019-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric	Chain A 43–318（276 aa） Chain B 43–318（276 aa）	Not recorded	MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 2.09 Å R-free 0.244
6W0Q APE1 endonuclease product complex D148E 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: tetrameric	Chain A 43–318（276 aa）	Mutation：D148E	MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.89 Å R-free 0.223
6W0Q APE1 endonuclease product complex D148E Deposited 2020-03-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：D148E	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.89 Å R-free 0.223
6W2P APE1 endonuclease product complex L104R Deposited 2020-03-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Mutation：L104R	MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.94 Å R-free 0.238
6W2P APE1 endonuclease product complex L104R Deposited 2020-03-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：L104R	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.94 Å R-free 0.238
6W3L APE1 exonuclease substrate complex wild-type Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.59 Å R-free 0.277
6W3L APE1 exonuclease substrate complex wild-type Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Not recorded	NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.59 Å R-free 0.277
6W3N APE1 exonuclease substrate complex D148E Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：D148E	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.69 Å R-free 0.308
6W3N APE1 exonuclease substrate complex D148E Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Mutation：D148E	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.69 Å R-free 0.308
6W3Q APE1 exonuclease substrate complex L104R Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：L104R	NA SODIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.49 Å R-free 0.259
6W3Q APE1 exonuclease substrate complex L104R Deposited 2020-03-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Mutation：L104R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.49 Å R-free 0.259
6W3U APE1 exonuclease substrate complex R237C Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：R237C	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.40 Å R-free 0.250
6W3U APE1 exonuclease substrate complex R237C Deposited 2020-03-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Mutation：R237C	EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.40 Å R-free 0.250
6W43 APE1 AP-endonuclease product complex R237C Deposited 2020-03-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Mutation：R237C	EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.99 Å R-free 0.224
6W43 APE1 AP-endonuclease product complex R237C Deposited 2020-03-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：R237C	EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2	Resolution 1.99 Å R-free 0.224
6W4I APE1 Y269A product complex with abasic DNA Deposited 2020-03-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Mutation：Y269A, C138A	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；24% PEG 3350, 0.1 M Bis Tris Propane (pH 6.5), 0.2 M Sodium Fluoride	Resolution 2.20 Å R-free 0.227
6W4I APE1 Y269A product complex with abasic DNA Deposited 2020-03-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：Y269A, C138A	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；24% PEG 3350, 0.1 M Bis Tris Propane (pH 6.5), 0.2 M Sodium Fluoride	Resolution 2.20 Å R-free 0.227
6W4T APE1 Y269A phosphorothioate substrate complex with abasic DNA Deposited 2020-03-11	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 43–318（276 aa）	Mutation：Y269A, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride	Resolution 2.77 Å R-free 0.274
6W4T APE1 Y269A phosphorothioate substrate complex with abasic DNA Deposited 2020-03-11	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 43–318（276 aa）	Mutation：Y269A, C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride	Resolution 2.77 Å R-free 0.274
7LPG APE1 product complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000	Resolution 2.08 Å R-free 0.263
7LPG APE1 product complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 43–318（276 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000	Resolution 2.08 Å R-free 0.263
7LPH APE1 Mn-bound product complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000	Resolution 1.99 Å R-free 0.237
7LPH APE1 Mn-bound product complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 43–318（276 aa）	Mutation：C138A	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000	Resolution 1.99 Å R-free 0.237
7LPI APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000	Resolution 2.05 Å R-free 0.245
7LPI APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 43–318（276 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000	Resolution 2.05 Å R-free 0.245
7LPJ APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：C138A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000	Resolution 2.56 Å R-free 0.248
7LPJ APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 43–318（276 aa）	Mutation：C138A	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000	Resolution 2.56 Å R-free 0.248
7MCR Human Apex/Ref1 homodimer formed under oxidative condition Deposited 2021-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 44–318（275 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；100 mM MES/ sodium hydroxide, 200 mM calcium acetate, 20% W/V PEG 8000	Resolution 1.90 Å R-free 0.233
7MEV Human Apex/Ref1 monomer with C138A mutation Deposited 2021-04-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–318（275 aa）	Mutation：C138A	MG MAGNESIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；20 %w/v PEG 3350, 200 mM Sodium nitrate	Resolution 1.60 Å R-free 0.196
7SUV APE1 exonuclease substrate complex with 8oxoG opposite A Deposited 2021-11-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：E96Q, C138A, D210N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 1.99 Å R-free 0.265
7SUV APE1 exonuclease substrate complex with 8oxoG opposite A Deposited 2021-11-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Mutation：E96Q, C138A, D210N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 1.99 Å R-free 0.265
7SVB APE1 exonuclease substrate complex with 8oxoG opposite C Deposited 2021-11-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：E96Q, C138A, D210N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.24 Å R-free 0.245
7SVB APE1 exonuclease substrate complex with 8oxoG opposite C Deposited 2021-11-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–318（276 aa）	Mutation：E96Q, C138A, D210N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride	Resolution 2.24 Å R-free 0.245
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–318（280 aa）	Not recorded	GID 5-nitro-1H-indole-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate	Resolution 1.43 Å R-free 0.270
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 39–318（280 aa）	Not recorded	GID 5-nitro-1H-indole-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate	Resolution 1.43 Å R-free 0.270
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 39–318（280 aa）	Not recorded	GID 5-nitro-1H-indole-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate	Resolution 1.43 Å R-free 0.270
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 39–318（280 aa）	Not recorded	GID 5-nitro-1H-indole-2-carboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate	Resolution 1.43 Å R-free 0.270
7TC3 Human APE1 in the apo form Deposited 2021-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–318（280 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate	Resolution 1.25 Å R-free 0.178
7TR7 APE1 product complex with abasic ssDNA Deposited 2022-01-28	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: dimeric	Chain A 43–318（276 aa）	Mutation：C138A	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.05M KCl, 0.05M sodium cacodylate pH 6, 10% PEG 8,000, 5mM spermine, 5mM L-Argininamide dihydrochloride	Resolution 2.00 Å R-free 0.215
7TR7 APE1 product complex with abasic ssDNA Deposited 2022-01-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 43–318（276 aa）	Mutation：C138A	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.05M KCl, 0.05M sodium cacodylate pH 6, 10% PEG 8,000, 5mM spermine, 5mM L-Argininamide dihydrochloride	Resolution 2.00 Å R-free 0.215
7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01	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 1–318（318 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9DP1 APE1 N174A Substrate Complex with Abasic DNA Deposited 2024-09-20	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 43–318（276 aa）	Mutation：tr1-42, C138A, N174A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000	Resolution 2.29 Å R-free 0.251
9DP1 APE1 N174A Substrate Complex with Abasic DNA Deposited 2024-09-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：tr1-42, C138A, N174A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000	Resolution 2.29 Å R-free 0.251
9DP2 APE1 N174A Product Complex with Abasic DNA Deposited 2024-09-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Mutation：tr1-42, C138A, N174A	MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000	Resolution 1.99 Å R-free 0.203
9DP2 APE1 N174A Product Complex with Abasic DNA Deposited 2024-09-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 43–318（276 aa）	Mutation：tr1-42, C138A, N174A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000	Resolution 1.99 Å R-free 0.203
9DP4 APE1 N174Q Product Complex with Abasic DNA Deposited 2024-09-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 43–318（276 aa）	Mutation：tr1-42, C138A, N174Q	PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM HEPES free acid, 200 mM ammonium acetate, 25% PEG3350	Resolution 2.25 Å R-free 0.248
9DP4 APE1 N174Q Product Complex with Abasic DNA Deposited 2024-09-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 43–318（276 aa）	Mutation：tr1-42, C138A, N174Q	PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM HEPES free acid, 200 mM ammonium acetate, 25% PEG3350	Resolution 2.25 Å R-free 0.248
9RQS Human APE1 in complex with DNA Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 39–318（280 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M ammonium sulfate, 0.1 M Na HEPES pH 7, 20% w/v PEG 4000	Resolution 1.70 Å R-free 0.228

66 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APEX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 43–318 Author chain B； PDBConstruct 1–276； UniProt 43–318

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	9dp3
Deposition date deposition_date	2024-09-20
Structure title title	APE1 N174D Product Complex with Abasic DNA
Keywords keywords	APE1, APEX1, Endonuclease, DNA Repair, HYDROLASE-DNA complex; HYDROLASE/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	30.67 Å
Radius of gyration Rg (electron density) rg_electron	29.61 Å
Forward intensity I(0) i0	105060000.00
Molecular weight molecular_weight	73430.0 kDa
Excluded volume excluded_volume	88498 Å³
Envelope volume envelope_volume	111910 Å³
Hydration-shell volume shell_volume	32799 Å³
Envelope diameter envelope_diameter	116.7 Å
Shell Rg shell_rg	35.28 Å
Envelope Rg envelope_rg	29.82 Å
Shape Rg shape_rg	29.55 Å
Total Rg total_rg	30.27 Å
Total atoms total_atoms	5128
Residues n_residues	583
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	107.8 Å
Rg (real space) rg_real	30.87 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	1.0510e+08
I(0) uncertainty (real space) i0_real_error	1.7590e+06
Rg (reciprocal space) rg_reciprocal	30.78 Å
I(0) (reciprocal space) i0_reciprocal	105100000.0000
Solution quality estimate total_estimate	0.8463
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.522
Kurtosis Kurtosis kurtosis	-0.110
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14530000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.889

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA repair nuclease/redox regulator APEX1, mitochondrial
Molecular weight formula_weight	31157.5 kDa
Mutation mutation	tr1-42, C138A, N174D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5445

ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPDAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

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

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(P(3DR)PCPGPAPCPGPGPAPTPCP*C)-3') ;
Molecular weight formula_weight	3210.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

NCGACGGATCC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3') ;
Molecular weight formula_weight	3061.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

GCTGATGCGC

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(GPGPAPTPCPCPGPTPCPGPGPGPCPGPCPAPTPCPAPGP*C)-3') ;
Molecular weight formula_weight	6465.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GGATCCGTCGGGCGCATCAGC

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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8. Citations (1)

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Unit-cell length a length_a	44.205 Å
Unit-cell length b length_b	60.834 Å
Unit-cell length c length_c	73.619 Å
Unit-cell angle α angle_alpha	82.55 °
Unit-cell angle β angle_beta	77.17 °
Unit-cell angle γ angle_gamma	85.85 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	24.950 Å
R factor r_factor	0.2546
R_work r_work	0.2534
R_free r_free	0.2744

fit	/app/data/saxs_computation/dp/9dp3/9dp3.fit
pddf	/app/data/pr_computation/dp/9dp3/9dp3.pr.out
profile	/app/data/saxs_computation/dp/9dp3/9dp3.dat

APE1 N174D Product Complex with Abasic DNA

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

DNA repair nuclease/redox regulator APEX1, mitochondrial

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)