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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

Method: SOLUTION NMR Dmax: 49.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THIOREDOXIN

Homo sapiens

UniProt P10599

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–104 Mutation：CHAIN A, C35A, C62A, C69A, C73A REF-1 PEPTIDE × 1 （P27695） SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

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 1CQH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AIU HUMAN THIOREDOXIN (D60N MUTANT, REDUCED FORM) Deposited 1997-04-25 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Mutation：D60N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.8；pH 3.8
Resolution 2.00 Å R-free 0.240
1AUC HUMAN THIOREDOXIN (OXIDIZED WITH DIAMIDE) Deposited 1997-08-22 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.10 Å R-free 0.270
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 Parsed fields agree Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Mutation：CHAIN A, C35A, C62A, C69A, C73A No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1ERT HUMAN THIOREDOXIN (REDUCED FORM) Deposited 1996-02-07 Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.240
1ERU HUMAN THIOREDOXIN (OXIDIZED FORM) Deposited 1996-02-07 Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.330
1ERV HUMAN THIOREDOXIN MUTANT WITH CYS 73 REPLACED BY SER (REDUCED FORM) Deposited 1996-02-07 Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Mutation：C73S No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å R-free 0.240
1ERW HUMAN THIOREDOXIN DOUBLE MUTANT WITH CYS 32 REPLACED BY SER AND CYS 35 REPLACED BY SER Deposited 1996-02-07 Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Mutation：C32S, C35S No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å R-free 0.260
1M7T Solution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability Deposited 2002-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 0–65（66 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；308 K
NMR sample composition 1 mM protein in 100 mM sodium phosphate buffer (pH 7.0), 20 M EDTA, 0.02% sodium azide, and 10% D2O. | 90% H2O/10% D2O
Resolution not provided
1MDI HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN MUTANT HUMAN THIOREDOXIN AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB Deposited 1995-02-27 Different mutation/modification Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1MDJ 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 NFKB (RESIDUES 56-68 OF THE P50 SUBUNIT OF NFKB) Deposited 1995-02-27 Different mutation/modification Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1MDK 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 NFKB (RESIDUES 56-68 OF THE P50 SUBUNIT OF NFKB) Deposited 1995-02-27 Different mutation/modification Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TRS THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES OF THE OXIDIZED AND REDUCED STATES OF HUMAN THIOREDOXIN Deposited 1994-05-10 Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TRU THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES OF THE OXIDIZED AND REDUCED STATES OF HUMAN THIOREDOXIN Deposited 1994-05-10 Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TRV THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES OF THE OXIDIZED AND REDUCED STATES OF HUMAN THIOREDOXIN Deposited 1994-05-10 Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TRW THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES OF THE OXIDIZED AND REDUCED STATES OF HUMAN THIOREDOXIN Deposited 1994-05-10 Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2IFQ Crystal structure of S-nitroso thioredoxin Deposited 2006-09-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 0–104（105 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.206
2IFQ Crystal structure of S-nitroso thioredoxin Deposited 2006-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 0–104（105 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.206
2IFQ Crystal structure of S-nitroso thioredoxin Deposited 2006-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 0–104（105 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EOH ETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.206
2IIY Crystal structure of S-nitroso thioredoxin Deposited 2006-09-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 0–104（105 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；32% PEG 1500, 50 mM sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.239
3E3E Human Thioredoxin Double Mutant C35S,C73R Deposited 2008-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：C35S, C73R P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；292 K；0.1 M Na acetate, pH 4.6, and 30 % (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.01 Å R-free 0.261
3E3E Human Thioredoxin Double Mutant C35S,C73R Deposited 2008-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：C35S, C73R P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；292 K；0.1 M Na acetate, pH 4.6, and 30 % (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.01 Å R-free 0.261
3KD0 Human thioredoxin C35S,C62S,C69S,C73S mutant showing cadmium chloride bound to the active site Deposited 2009-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：C35S, C62S, C69S, C73S CL CHLORIDE ION × 4 CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；292 K；0.16M Cadmium Chloride, 2.0M ammonium sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.70 Å R-free 0.279
3KD0 Human thioredoxin C35S,C62S,C69S,C73S mutant showing cadmium chloride bound to the active site Deposited 2009-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–105（105 aa）
Mutation：C35S, C62S, C69S, C73S CL CHLORIDE ION × 8 CD CADMIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；292 K；0.16M Cadmium Chloride, 2.0M ammonium sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.70 Å R-free 0.279
3M9J Crystal structure of human thioredoxin C69/73S double mutant, reduced form Deposited 2010-03-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：C69S, C73S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；30% PEG 4000, 200 mM ammonium acetate, 100 mM sodium citrate, 5 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.10 Å R-free 0.172
3M9J Crystal structure of human thioredoxin C69/73S double mutant, reduced form Deposited 2010-03-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：C69S, C73S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；30% PEG 4000, 200 mM ammonium acetate, 100 mM sodium citrate, 5 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.10 Å R-free 0.172
3M9K Crystal structure of human thioredoxin C69/73S double-mutant, oxidized form Deposited 2010-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：C69S, C73S SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；1.8 M ammonium sulfate, 100 mM MES, 10 mM CoCl2, 2 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.211
3M9K Crystal structure of human thioredoxin C69/73S double-mutant, oxidized form Deposited 2010-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：C69S, C73S SO4 SULFATE ION × 3 D1D (4S,5S)-1,2-DITHIANE-4,5-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；1.8 M ammonium sulfate, 100 mM MES, 10 mM CoCl2, 2 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.211
3M9K Crystal structure of human thioredoxin C69/73S double-mutant, oxidized form Deposited 2010-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Mutation：C69S, C73S Mutation：C69S, C73S SO4 SULFATE ION × 8 D1D (4S,5S)-1,2-DITHIANE-4,5-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；1.8 M ammonium sulfate, 100 mM MES, 10 mM CoCl2, 2 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.211
3QFA Crystal structure of the human thioredoxin reductase-thioredoxin complex Deposited 2011-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–105（104 aa）
Chain D 2–105（104 aa）
Mutation：C35S, C73S Mutation：C35S, C73S FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297.15 K；15% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.15 K
Resolution 2.20 Å R-free 0.283
3QFB Crystal structure of the human thioredoxin reductase-thioredoxin complex Deposited 2011-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–105（104 aa）
Chain D 2–105（104 aa）
Mutation：C35S, C73S Mutation：C35S, C73S FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；297.15 K；15% PEG 4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 297.15K
Resolution 2.60 Å R-free 0.297
3TRX HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REDUCED RECOMBINANT HUMAN THIOREDOXIN IN SOLUTION Deposited 1990-12-17 Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
4LL1 The structure of the TRX and TXNIP complex Deposited 2013-07-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：C35A Mutation：C35A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；0.16M tri-sodium citrate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K
Resolution 2.00 Å R-free 0.288
4LL4 The structure of the TRX and TXNIP complex Deposited 2013-07-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：C35A Mutation：C35A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；0.16M tri-sodium citrate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K
Resolution 2.70 Å R-free 0.264
4OO4 Crystal Structure of Human Thioredoxin Mutant Deposited 2014-01-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：Q63A, C69S, C73S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；289 K；20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 0.97 Å R-free 0.165
4OO4 Crystal Structure of Human Thioredoxin Mutant Deposited 2014-01-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：Q63A, C69S, C73S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；289 K；20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 0.97 Å R-free 0.165
4OO4 Crystal Structure of Human Thioredoxin Mutant Deposited 2014-01-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Mutation：Q63A, C69S, C73S Mutation：Q63A, C69S, C73S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；289 K；20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 0.97 Å R-free 0.165
4OO5 Crystal Structure of S-nitrosated Human Thioredoxin Mutant Deposited 2014-01-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：C69S, C73S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；289 K；21% PEG 3350, 0.1 M sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.54 Å R-free 0.248
4POK Crystal structures of thioredoxin with mesna at 2.5A resolution Deposited 2014-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% ethanol, 0.1 M Tris, 60 mg/mL Trx protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.296
4POK Crystal structures of thioredoxin with mesna at 2.5A resolution Deposited 2014-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% ethanol, 0.1 M Tris, 60 mg/mL Trx protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.296
4POK Crystal structures of thioredoxin with mesna at 2.5A resolution Deposited 2014-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% ethanol, 0.1 M Tris, 60 mg/mL Trx protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.296
4POK Crystal structures of thioredoxin with mesna at 2.5A resolution Deposited 2014-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% ethanol, 0.1 M Tris, 60 mg/mL Trx protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.296
4POK Crystal structures of thioredoxin with mesna at 2.5A resolution Deposited 2014-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% ethanol, 0.1 M Tris, 60 mg/mL Trx protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.296
4POK Crystal structures of thioredoxin with mesna at 2.5A resolution Deposited 2014-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% ethanol, 0.1 M Tris, 60 mg/mL Trx protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.52 Å R-free 0.296
4POL Crystal structures of thioredoxin with mesna at 2.8A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
4POL Crystal structures of thioredoxin with mesna at 2.8A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
4POL Crystal structures of thioredoxin with mesna at 2.8A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
4POL Crystal structures of thioredoxin with mesna at 2.8A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
4POL Crystal structures of thioredoxin with mesna at 2.8A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
4POL Crystal structures of thioredoxin with mesna at 2.8A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
4POM Crystal structures of thioredoxin with mesna at 1.85A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.261
4POM Crystal structures of thioredoxin with mesna at 1.85A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.261
4POM Crystal structures of thioredoxin with mesna at 1.85A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.261
4POM Crystal structures of thioredoxin with mesna at 1.85A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.261
4POM Crystal structures of thioredoxin with mesna at 1.85A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.261
4POM Crystal structures of thioredoxin with mesna at 1.85A resolution Deposited 2014-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–105（105 aa）
Chain B 1–105（105 aa）
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K Mutation：E13K, D16K, E95K, E103K COM 1-THIOETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.261
4PUF Complex between the Salmonella T3SS effector SlrP and its human target thioredoxin-1 Deposited 2014-03-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–105（105 aa）
Chain D 1–105（105 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；291 K；15% PEG 4000, 0.2M NaCl, 0.1M MgCl2, 0.1M Hepes, 216 M SlrP, 430 M Trx1, pH 7.8, VAPOR DIFFUSION, temperature 291K
Resolution 3.30 Å R-free 0.308
4TRX HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REDUCED RECOMBINANT HUMAN THIOREDOXIN IN SOLUTION Deposited 1990-12-17 Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
5DQY A fully oxidized human thioredoxin Deposited 2015-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Not recorded BEZ BENZOIC ACID × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294.15 K；Ammonium citrate, Bis-Tris propane
Resolution 1.40 Å R-free 0.209
5DQY A fully oxidized human thioredoxin Deposited 2015-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–105（104 aa）
Not recorded BEZ BENZOIC ACID × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294.15 K；Ammonium citrate, Bis-Tris propane
Resolution 1.40 Å R-free 0.209

34 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIO_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–105； UniProt 1–104

REF-1 PEPTIDE

OrganismNot specified

UniProt P27695

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 58–70 Fragment：RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB THIOREDOXIN × 1 （P10599） SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

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 1CQH 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 oligomeric state Different ligand/ion Different experimental method 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 Parsed fields agree 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different experimental method 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 construct Different oligomeric state Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 method 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 oligomeric state Different experimental method 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 method 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 oligomeric state Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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
9DP3 APE1 N174D Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method 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, 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 123 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APEX1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–13； UniProt 58–70

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

SAXS scattering curve SAXS Profile

SAXS profile for 1cqh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cqh
Deposition date deposition_date1996-04-02
Structure title titleHIGH 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
Keywords keywordsCOMPLEX, ELECTRON TRANSPORT/PEPTIDE, COMPLEX (ELECTRON TRANSPORT-PEPTIDE) COMPLEX; COMPLEX (ELECTRON TRANSPORT/PEPTIDE)
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.00 Å
Radius of gyration Rg (electron density) rg_electron13.53 Å
Forward intensity I(0) i03294420.00
Molecular weight molecular_weight12978.0 kDa
Excluded volume excluded_volume16399 ų
Envelope volume envelope_volume18690 ų
Hydration-shell volume shell_volume11768 ų
Envelope diameter envelope_diameter48.8 Å
Shell Rg shell_rg19.28 Å
Envelope Rg envelope_rg13.90 Å
Shape Rg shape_rg13.48 Å
Total Rg total_rg14.99 Å
Total atoms total_atoms1817
Residues n_residues118
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax49.1 Å
Rg (real space) rg_real14.91 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real3.2940e+06
I(0) uncertainty (real space) i0_real_error3.7960e+04
Rg (reciprocal space) rg_reciprocal14.92 Å
I(0) (reciprocal space) i0_reciprocal3294000.0000
Solution quality estimate total_estimate0.7965
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.0 Å
Skewness Skewness skewness0.185
Kurtosis Kurtosis kurtosis-0.258
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha889000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cqha_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.1 — Thioltransferase

CATH v4.4 (1 domains)

Domain ID domain_id1cqhA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
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8. Citations (4)

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9. Files and Curves (10)