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9osw

Tetrameric POLQ Helicase-like Domain Bound to Cmpd 19, a Small-Molecule ATPase Inhibitor and Drug Candidate Analog

Method: ELECTRON MICROSCOPY Dmax: 144.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase theta

Homo sapiens

UniProt O75417

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–904 Chain B； UniProt 1–904 Chain C； UniProt 1–904 Chain D； UniProt 1–904 Fragment：N-terminal domain A1CER (3M)-2'-chloro-N-{5-[(1S,2S)-2-(4-cyanophenyl)cyclopropyl]-1,3,4-thiadiazol-2-yl}-5'-methoxy[3,4'-bipyridine]-4-carboxamide × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；20 mM HEPES pH 7.5, 300 mM NaCl, 1 mM TCEP, 5% glycerol cryo-EM vitrification conditions：Cryogen ETHANE；3 microL drop of sample suspension is applied to an EM grid that has been plasma-cleaned using a Gatan Solarus. After blotting the sample away with filter paper, grids are plunge-frozen in liquid ethane. Grids are stored under liquid nitrogen until transferred to the transmission electron microscope for imaging. Resolution 2.67 Å

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 9OSW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4X0P Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog Deposited 2014-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1792–2590（799 aa） Fragment：UNP residues 1792-2590
Not recorded GOL GLYCEROL × 2 CA CALCIUM ION × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG 2000mme, MPD, potassium chloride, calcium chloride, TRIS buffer, glycerol
Resolution 3.91 Å R-free 0.302
4X0P Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog Deposited 2014-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1792–2590（799 aa） Fragment：UNP residues 1792-2590
Not recorded GOL GLYCEROL × 2 CA CALCIUM ION × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG 2000mme, MPD, potassium chloride, calcium chloride, TRIS buffer, glycerol
Resolution 3.91 Å R-free 0.302
4X0P Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog Deposited 2014-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1792–2590（799 aa） Fragment：UNP residues 1792-2590
Not recorded GOL GLYCEROL × 2 CA CALCIUM ION × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG 2000mme, MPD, potassium chloride, calcium chloride, TRIS buffer, glycerol
Resolution 3.91 Å R-free 0.302
4X0P Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog Deposited 2014-11-21 Different construct Different mutation/modification 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: trimeric
Chain D 1792–2590（799 aa） Fragment：UNP residues 1792-2590
Not recorded GOL GLYCEROL × 2 CA CALCIUM ION × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG 2000mme, MPD, potassium chloride, calcium chloride, TRIS buffer, glycerol
Resolution 3.91 Å R-free 0.302
4X0Q Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP Deposited 2014-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1819–2590（772 aa） Fragment：UNP residues 1815-2590
Not recorded GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG 2000mme, MPD, potassium chloride, TRIS buffer, glycerol
Resolution 3.90 Å R-free 0.316
4X0Q Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP Deposited 2014-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1819–2590（772 aa） Fragment：UNP residues 1815-2590
Not recorded GOL GLYCEROL × 2 MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG 2000mme, MPD, potassium chloride, TRIS buffer, glycerol
Resolution 3.90 Å R-free 0.316
5A9F Crystal structure of the Helicase domain of human DNA polymerase theta in complex with ADP Deposited 2015-07-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 67–894（828 aa） Fragment：HELICASE DOMAIN, RESIDUES 67-894
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 4 K POTASSIUM ION × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions 19% PEG 3350, 0.2M POTASSIUM CITRATE TRIBASIC
Resolution 3.20 Å R-free 0.273
5A9J Crystal structure of the Helicase domain of human DNA polymerase theta, apo-form Deposited 2015-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–894（894 aa） Fragment：HELICASE DOMAIN, UNP RESIDUES 1-894
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.2M NACL, 20% PEG 6K, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.0
Resolution 3.55 Å R-free 0.265
5A9J Crystal structure of the Helicase domain of human DNA polymerase theta, apo-form Deposited 2015-07-21 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 1–894（894 aa） Fragment：HELICASE DOMAIN, UNP RESIDUES 1-894
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.2M NACL, 20% PEG 6K, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.0
Resolution 3.55 Å R-free 0.265
5A9J Crystal structure of the Helicase domain of human DNA polymerase theta, apo-form Deposited 2015-07-21 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 1–894（894 aa） Fragment：HELICASE DOMAIN, UNP RESIDUES 1-894
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.2M NACL, 20% PEG 6K, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.0
Resolution 3.55 Å R-free 0.265
5A9J Crystal structure of the Helicase domain of human DNA polymerase theta, apo-form Deposited 2015-07-21 Different construct Different mutation/modification 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 1–894（894 aa） Fragment：HELICASE DOMAIN, UNP RESIDUES 1-894
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.2M NACL, 20% PEG 6K, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.0
Resolution 3.55 Å R-free 0.265
5AGA Crystal structure of the Helicase domain of human DNA polymerase theta in complex with AMPPNP Deposited 2015-01-29 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 67–894（828 aa） Fragment：HELICASE DOMAIN, RESIDUES 67-894
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 FLC CITRATE ANION × 4 K POTASSIUM ION × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions 19% PEG 3350, 0.2M POTASSIUM CITRATE TRIBASIC
Resolution 2.90 Å R-free 0.264
5AGA Crystal structure of the Helicase domain of human DNA polymerase theta in complex with AMPPNP Deposited 2015-01-29 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 67–894（828 aa） Fragment：HELICASE DOMAIN, RESIDUES 67-894
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 FLC CITRATE ANION × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 19% PEG 3350, 0.2M POTASSIUM CITRATE TRIBASIC
Resolution 2.90 Å R-free 0.264
6XBU polymerase domain of polymerase-theta Deposited 2020-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1819–1860（42 aa）
Chain A 1068–1089（22 aa）
Chain A 1935–2145（211 aa）
Chain A 2176–2260（85 aa）
Chain A 2307–2512（206 aa）
Chain A 2527–2590（64 aa）
Not recorded DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) Ethanol
Resolution 3.29 Å R-free 0.281
7ZUS Crystal structure of ternary complex of Pol theta polymerase domain Deposited 2022-05-13 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 AAA 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate.
Resolution 2.26 Å R-free 0.238
7ZUS Crystal structure of ternary complex of Pol theta polymerase domain Deposited 2022-05-13 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 BBB 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate.
Resolution 2.26 Å R-free 0.238
7ZUS Crystal structure of ternary complex of Pol theta polymerase domain Deposited 2022-05-13 Different construct Different mutation/modification 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: trimeric
Chain CCC 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate.
Resolution 2.26 Å R-free 0.238
7ZX0 Crystal structure of Pol theta polymerase domain in complex with compound 5 Deposited 2022-05-19 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 AAA 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 K7X 2-[5-bromanyl-3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]oxy-~{N}-ethyl-~{N}-(3-methylphenyl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.99 Å R-free 0.252
7ZX0 Crystal structure of Pol theta polymerase domain in complex with compound 5 Deposited 2022-05-19 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 BBB 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.99 Å R-free 0.252
7ZX0 Crystal structure of Pol theta polymerase domain in complex with compound 5 Deposited 2022-05-19 Different construct Different mutation/modification 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: trimeric
Chain CCC 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.99 Å R-free 0.252
7ZX0 Crystal structure of Pol theta polymerase domain in complex with compound 5 Deposited 2022-05-19 Different construct Different mutation/modification 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: trimeric
Chain DDD 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.99 Å R-free 0.252
7ZX0 Crystal structure of Pol theta polymerase domain in complex with compound 5 Deposited 2022-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain EEE 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.99 Å R-free 0.252
7ZX0 Crystal structure of Pol theta polymerase domain in complex with compound 5 Deposited 2022-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain FFF 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.99 Å R-free 0.252
7ZX1 Crystal structure of Pol theta polymerase domain in complex with compound 22 Deposited 2022-05-19 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 AAA 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 K8I (2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.83 Å R-free 0.260
7ZX1 Crystal structure of Pol theta polymerase domain in complex with compound 22 Deposited 2022-05-19 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 BBB 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 K8I (2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.83 Å R-free 0.260
7ZX1 Crystal structure of Pol theta polymerase domain in complex with compound 22 Deposited 2022-05-19 Different construct Different mutation/modification 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: trimeric
Chain CCC 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 K8I (2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.83 Å R-free 0.260
7ZX1 Crystal structure of Pol theta polymerase domain in complex with compound 22 Deposited 2022-05-19 Different construct Different mutation/modification 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: trimeric
Chain DDD 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 K8I (2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.83 Å R-free 0.260
7ZX1 Crystal structure of Pol theta polymerase domain in complex with compound 22 Deposited 2022-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain EEE 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.83 Å R-free 0.260
7ZX1 Crystal structure of Pol theta polymerase domain in complex with compound 22 Deposited 2022-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain FFF 1820–2590（771 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate
Resolution 2.83 Å R-free 0.260
8E23 Human DNA polymerase theta in complex with allosteric inhibitor Deposited 2022-08-13 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 UAF N-methyl-N-phenyl[(3aM)-3-(trifluoromethyl)cyclopenta[c]pyrazol-2(1H)-yl]ethanethioamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；18.5 % PEG 3350; 0.2M diammonium tartrate
Resolution 2.59 Å R-free 0.295
8E23 Human DNA polymerase theta in complex with allosteric inhibitor Deposited 2022-08-13 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；18.5 % PEG 3350; 0.2M diammonium tartrate
Resolution 2.59 Å R-free 0.295
8E24 Human DNA polymerase theta in complex with allosteric inhibitor Deposited 2022-08-13 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 UA6 2-[2,4-bis(trifluoromethyl)phenyl]-N-phenyl-N-[3-(pyridazin-3-yl)prop-2-yn-1-yl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；16% PEG 3350, 0.2M diammonium tartrate, 2% glycerol
Resolution 2.34 Å R-free 0.266
8E24 Human DNA polymerase theta in complex with allosteric inhibitor Deposited 2022-08-13 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 UA6 2-[2,4-bis(trifluoromethyl)phenyl]-N-phenyl-N-[3-(pyridazin-3-yl)prop-2-yn-1-yl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；16% PEG 3350, 0.2M diammonium tartrate, 2% glycerol
Resolution 2.34 Å R-free 0.266
8GD7 Loop Deleted DNA Polymerase Theta Polymerase Domain in Complex with Double Strand DNA Overhang and Inhibitor Deposited 2023-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1819–2590（772 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 Z5X 2-(3-methyl-2-oxoimidazolidin-1-yl)-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)methylcarbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；0.24 M Sodium citrate, 18% (w/v) PEG 3350, 0.1 M Bis Tris Propane pH 7.5
Resolution 3.24 Å R-free 0.244
8W0A Human DNA polymerase theta helicase domain in complex with ssDNA, dimer form Deposited 2024-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–894（894 aa）
Chain C 1–894（894 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9ASJ Human DNA polymerase theta helicase domain in complex with AMP-PNP, dimer form Deposited 2024-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–894（894 aa）
Chain B 1–894（894 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9ASK Human DNA polymerase theta helicase domain dimer, apo-form Deposited 2024-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–894（894 aa）
Chain B 1–894（894 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9ASL Human DNA polymerase theta helicase domain tetramer, apo-form Deposited 2024-02-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–894（894 aa）
Chain B 1–894（894 aa）
Chain C 1–894（894 aa）
Chain D 1–894（894 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9AU5 Ternary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair Deposited 2024-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1792–2590（799 aa）
Not recorded DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
9AU8 Ternary complex of human DNA polymerase theta polymerase domain with a mismatched T:T base pair Deposited 2024-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1792–2590（799 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
9AU9 Ternary complex of human DNA polymerase theta polymerase domain with a mismatched T:G base pair Deposited 2024-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1792–2590（799 aa）
Not recorded DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9BH6 Human DNA polymerase theta helicase domain tetramer in the apo form Deposited 2024-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–894（893 aa）
Chain B 2–894（893 aa）
Chain C 2–894（893 aa）
Chain D 2–894（893 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 microliters of sample was applied to the surface of the grid, blotted with Whatman 1 filter paper until 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane pool cooled by liquid nitrogen using a manual plunge freezer.
Resolution 3.30 Å
9BH7 Human DNA polymerase theta helicase domain dimer in the apo form Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–894（893 aa）
Chain B 2–894（893 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 microliters of sample was applied to the surface of the grid, blotted with Whatman 1 filter paper until 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane pool cooled by liquid nitrogen using a manual plunge freezer.
Resolution 3.50 Å
9BH8 Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology searching conformation Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 2–894（893 aa）
Chain B 2–894（893 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 microliters of sample was applied to the surface of the grid, blotted with Whatman 1 filter paper until 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane bath cooled by liquid nitrogen.
Resolution 3.60 Å
9BH9 Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology aligning conformation Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 2–894（893 aa）
Chain B 2–894（893 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 microliters of sample was applied to the surface of the grid, blotted for 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane bath cooled by liquid nitrogen.
Resolution 3.50 Å
9BHA Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology annealed conformation Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 2–894（893 aa）
Chain B 2–894（893 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 microliters of sample was applied to the surface of the grid, blotted with Whatman 1 filter paper until 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane bath cooled by liquid nitrogen.
Resolution 3.50 Å
9BP9 Human DNA polymerase theta helicase domain in complex with inhibitor AB25583, dimer form Deposited 2024-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–894（894 aa）
Chain C 1–894（894 aa）
Not recorded WCN (4P)-N-{5-[(4-chlorophenyl)methoxy]-1,3,4-thiadiazol-2-yl}-4-(2-methoxyphenyl)pyridine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
9BPA Human DNA polymerase theta helicase domain in complex with inhibitor AB25583, tetramer form Deposited 2024-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–894（894 aa）
Chain C 1–894（894 aa）
Chain E 1–894（894 aa）
Chain G 1–894（894 aa）
Not recorded WCN (4P)-N-{5-[(4-chlorophenyl)methoxy]-1,3,4-thiadiazol-2-yl}-4-(2-methoxyphenyl)pyridine-3-carboxamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
9C5Q Human DNA polymerase theta helicase domain in microhomology annealed state 2, dimer form Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 68–891（824 aa）
Chain C 68–891（824 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9D6N Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor Deposited 2024-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1819–2590（772 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 A1A2C 2-{3-[(2R)-3-(dimethylamino)-2-hydroxypropyl]-2-oxoimidazolidin-1-yl}-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；0.1M Bis Tris Propane pH 7.5, 16% PEG 3350, 0.23M Sodium Citrate
Resolution 2.43 Å R-free 0.237
9D6N Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor Deposited 2024-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1819–2590（772 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 A1A2C 2-{3-[(2R)-3-(dimethylamino)-2-hydroxypropyl]-2-oxoimidazolidin-1-yl}-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；0.1M Bis Tris Propane pH 7.5, 16% PEG 3350, 0.23M Sodium Citrate
Resolution 2.43 Å R-free 0.237
9D6O Loop-Deleted DNA Polymerase Theta Polymerase Domain in Complex with a dsDNA Overhang and an Allosteric Inhibitor Deposited 2024-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1819–2590（772 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 A1A2D 2-[3-(2-hydroxyethyl)-2-oxoimidazolidin-1-yl]-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；0.1M Bis Tris Propane pH 7.5, 18% (w/v) PEG 3350, 0.29M Sodium Tartrate
Resolution 3.31 Å R-free 0.234
9OSY Tetrameric POLQ Helicase-like Domain Bound to Cmpd 36, a Small-Molecule ATPase Inhibitor and Drug Candidate Analog Deposited 2025-05-26 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–904（904 aa） Fragment：N-terminal domain
Chain B 1–904（904 aa） Fragment：N-terminal domain
Chain C 1–904（904 aa） Fragment：N-terminal domain
Chain D 1–904（904 aa） Fragment：N-terminal domain
Not recorded A1CEQ (2P)-N-[5-(cyclopropylethynyl)-1,3,4-thiadiazol-2-yl]-2-[2-(difluoromethyl)-5-methoxypyridin-4-yl]-4-[(4-hydroxyoxan-4-yl)ethynyl]benzamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 300 mM NaCl, 1 mM TCEP, 5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE；3 microL drop of sample suspension is applied to an EM grid that has been plasma-cleaned using a Gatan Solarus. After blotting the sample away with filter paper, grids are plunge-frozen in liquid ethane. Grids are stored under liquid nitrogen until transferred to the transmission electron microscope for imaging.
Resolution 2.90 Å
9YSH Allosteric inhibitor of human DNA polymerase theta Deposited 2025-10-18 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 A1CZX N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)pyridine-3-carboxamide × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；14% PEG 3350, 200 mM sodium-potassium tartrate, 6% glycerol, 0.02% sucrose monolaurate, and 20 mM spermine tetrahydrochloride
Resolution 2.71 Å R-free 0.251
9YSH Allosteric inhibitor of human DNA polymerase theta Deposited 2025-10-18 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 A1CZX N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)pyridine-3-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；14% PEG 3350, 200 mM sodium-potassium tartrate, 6% glycerol, 0.02% sucrose monolaurate, and 20 mM spermine tetrahydrochloride
Resolution 2.71 Å R-free 0.251
9YSI Covalent allosteric inhibitor of human DNA polymerase theta Deposited 2025-10-18 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 2 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 3 A1CZ4 N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)-2-(ethanesulfonamido)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；22% PEG 3350, 200 mM sodium-potassium tartrate, 3% glycerol, 0.02% sucrose monolaurate, and 20 mM spermine tetrahydrochloride
Resolution 2.00 Å R-free 0.211
9YSI Covalent allosteric inhibitor of human DNA polymerase theta Deposited 2025-10-18 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 1818–2590（773 aa）
Not recorded MG MAGNESIUM ION × 1 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 A1CZ4 N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)-2-(ethanesulfonamido)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；22% PEG 3350, 200 mM sodium-potassium tartrate, 3% glycerol, 0.02% sucrose monolaurate, and 20 mM spermine tetrahydrochloride
Resolution 2.00 Å R-free 0.211

32 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOLQ_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–904； UniProt 1–904 Author chain B； PDBConstruct 1–904； UniProt 1–904 Author chain C； PDBConstruct 1–904； UniProt 1–904 Author chain D； PDBConstruct 1–904； UniProt 1–904

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 9osw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9osw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9osw
Deposition date deposition_date2025-05-26
Structure title titleTetrameric POLQ Helicase-like Domain Bound to Cmpd 19, a Small-Molecule ATPase Inhibitor and Drug Candidate Analog
Keywords keywordsTheta-mediated end-joining DNA-dependent ATPase DNA repair Inhibitor co-complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.88 Å
Radius of gyration Rg (electron density) rg_electron48.42 Å
Forward intensity I(0) i01217990000.00
Molecular weight molecular_weight300870.0 kDa
Excluded volume excluded_volume380890 ų
Envelope volume envelope_volume527820 ų
Hydration-shell volume shell_volume88570 ų
Envelope diameter envelope_diameter145.8 Å
Shell Rg shell_rg54.07 Å
Envelope Rg envelope_rg48.04 Å
Shape Rg shape_rg48.48 Å
Total Rg total_rg48.41 Å
Total atoms total_atoms42637
Residues n_residues2696
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 dmax144.0 Å
Rg (real space) rg_real48.58 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real1.2180e+09
I(0) uncertainty (real space) i0_real_error1.9700e+07
Rg (reciprocal space) rg_reciprocal48.88 Å
I(0) (reciprocal space) i0_reciprocal1218000000.0000
Solution quality estimate total_estimate0.8580
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.5 Å
Skewness Skewness skewness0.068
Kurtosis Kurtosis kurtosis-0.712
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha189400000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.987; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.203
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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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8. Citations (1)

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9. Files and Curves (10)