Current Protein Identity：P27695
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | 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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 |
| 9DP3 APE1 N174D Product Complex with Abasic DNA Deposited 2024-09-20 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
Chain A
43–318（276 aa）
|
Mutation：tr1-42, C138A, N174D | 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 |
| 9DP3 APE1 N174D Product Complex with Abasic DNA Deposited 2024-09-20 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
43–318（276 aa）
|
Mutation：tr1-42, C138A, N174D | No recorded non-water small molecule | 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 |
| 9DP4 APE1 N174Q Product Complex with Abasic DNA Deposited 2024-09-20 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers |
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 |