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4zzy

Structure of human PARP2 catalytic domain bound to an isoindolinone inhibitor

Method: X-RAY DIFFRACTION Dmax: 70.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

POLY [ADP-RIBOSE] POLYMERASE 2

HOMO SAPIENS

UniProt Q9UGN5

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 223–583 Fragment：CATALYTIC DOMAIN, UNP RESIDUES 223-583 D7N 2-[1-(4,4-Difluorocyclohexyl)-piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：25% PEG4000, 0.2M MAGNESIUM CLORIDE, 0.1 M TRIS PH 8.5 Resolution 2.20 Å R-free 0.280

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 4ZZY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3KCZ Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide Deposited 2009-10-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–579（345 aa） Fragment：Catalytic domain
Not recorded 3AB 3-aminobenzamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；22% PEG 3350, 0.1M Tris-HCl, 0.01M 3-aminobenzamide, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.237
3KCZ Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide Deposited 2009-10-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 235–579（345 aa） Fragment：Catalytic domain
Not recorded 3AB 3-aminobenzamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；22% PEG 3350, 0.1M Tris-HCl, 0.01M 3-aminobenzamide, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.237
3KJD Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888 Deposited 2009-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–579（345 aa） Fragment：catalytic domain
Not recorded 78P (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 3350, 0.1M Tris, 0.25M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.95 Å R-free 0.232
3KJD Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888 Deposited 2009-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 235–579（345 aa） Fragment：catalytic domain
Not recorded 78P (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 3350, 0.1M Tris, 0.25M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.95 Å R-free 0.232
4PJV Structure of PARP2 catalytic domain bound to inhibitor BMN 673 Deposited 2014-05-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–579（345 aa） Fragment：PARP2 HELICAL AND CATALYTIC DOMAINS (UNP residues 235-579)
Not recorded 2YQ (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；(W/V) POLYETHYLENE GLYCOL 3350, 333 mM SODIUM CHLORIDE.
Resolution 2.50 Å R-free 0.287
4PJV Structure of PARP2 catalytic domain bound to inhibitor BMN 673 Deposited 2014-05-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 235–579（345 aa） Fragment：PARP2 HELICAL AND CATALYTIC DOMAINS (UNP residues 235-579)
Not recorded 2YQ (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；(W/V) POLYETHYLENE GLYCOL 3350, 333 mM SODIUM CHLORIDE.
Resolution 2.50 Å R-free 0.287
4TVJ HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB Deposited 2014-06-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 235–579（345 aa）
Not recorded 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG3350, 0.1M Tris
Resolution 2.10 Å R-free 0.231
4TVJ HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB Deposited 2014-06-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 235–579（345 aa）
Not recorded 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG3350, 0.1M Tris
Resolution 2.10 Å R-free 0.231
4ZZX Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor Deposited 2015-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 223–583（361 aa） Fragment：CATALYTIC DOMAIN, UNP RESIDUES 223-583
Not recorded FSU 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；25% PEG4000, 0.2M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 8.5, 277K
Resolution 1.65 Å R-free 0.244
4ZZX Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor Deposited 2015-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 223–583（361 aa） Fragment：CATALYTIC DOMAIN, UNP RESIDUES 223-583
Not recorded FSU 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；25% PEG4000, 0.2M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 8.5, 277K
Resolution 1.65 Å R-free 0.244
5D5K Crystal Structure NLS from human PARP-2 complexed with Importin alpha delta IBB Deposited 2015-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–78（78 aa） Fragment：unp residues 1-78
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；0.6-0.7M sodium citrate, 0.1M sodium citrate buffer pH 5.6, and 7-10mM DTT
Resolution 1.90 Å R-free 0.171
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
6F1K Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate Deposited 2017-11-22 Different construct 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 90–218（129 aa）
Not recorded GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277 K；PEG MME 5000 0.1 M Na-acetate ethylene glyco
Resolution 2.20 Å R-free 0.250
6F5B Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate Deposited 2017-12-01 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: hexameric
Chain A 90–218（129 aa）
Chain B 90–218（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；12 % v/v Polypropylene glycol 400 0.1 M Na-acetate 3 % 2 propanol
Resolution 2.80 Å R-free 0.274
6F5F Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate Deposited 2017-12-01 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 90–218（129 aa）
Chain C 90–218（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Na-formate 20 % PEG 3350 20 % glycerol
Resolution 2.98 Å R-free 0.275
6F5F Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate Deposited 2017-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain B 90–218（129 aa）
Chain D 90–218（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Na-formate 20 % PEG 3350 20 % glycerol
Resolution 2.98 Å R-free 0.275
6TX3 HPF1 bound to catalytic fragment of PARP2 Deposited 2020-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 230–253（24 aa）
Chain B 348–583（236 aa）
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6, 25% v/v pentaerythritol propoxylate (5/4 PO/OH)
Resolution 2.96 Å R-free 0.260
6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain U 1–570（570 aa）
Chain V 1–570（570 aa）
Mutation：Q112R, F113D Mutation：Q112R, F113D No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2s, blot force 0
Resolution 10.50 Å
6X0L Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain P 1–570（570 aa）
Chain R 1–570（570 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6X0M Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain P 1–570（570 aa）
Chain p 1–570（570 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain P 1–570（570 aa）
Chain R 1–570（570 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
7AEO Human ARTD2 in complex with DNA oligonucleotides Deposited 2020-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 90–583（494 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Sample was crystallized in 0.1 M MES pH 6.5 and 1 M ammonium sulfate. Cryo solution was a mixture of 10% (v/v) glycerol, 10% (v/v) diethylene glycol, and 10% (v/v) 2-propanol with the crystallization conditions
Resolution 2.80 Å R-free 0.271
7R59 PARP2 catalytic domain in complex with OUL245 Deposited 2022-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–583（349 aa）
Not recorded GOL GLYCEROL × 1 I5F [1,2,4]triazolo[3,4-b][1,3]benzothiazol-6-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Tris pH 9.5 and 20% PEG 3350
Resolution 2.00 Å R-free 0.238
8HE8 Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Deposited 2022-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 231–581（351 aa）
Not recorded GOL GLYCEROL × 1 1WI 1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5
Resolution 3.05 Å R-free 0.256
8HE8 Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Deposited 2022-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 231–581（351 aa）
Not recorded GOL GLYCEROL × 1 1WI 1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5
Resolution 3.05 Å R-free 0.256
8HE8 Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Deposited 2022-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 231–581（351 aa）
Not recorded 1WI 1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5
Resolution 3.05 Å R-free 0.256
8HKN Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to approved drug Fluzoparib Deposited 2022-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 25I Fluzoparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.50 Å R-free 0.261
8HKN Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to approved drug Fluzoparib Deposited 2022-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 25I Fluzoparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.50 Å R-free 0.261
8HKO Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib Deposited 2022-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 5 RPB Rucaparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.211
8HKO Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib Deposited 2022-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 RPB Rucaparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.211
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 2 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 5 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 2 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 3 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HLJ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib (AZD2281) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296.5 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.24 Å R-free 0.247
8HLJ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib (AZD2281) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296.5 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.24 Å R-free 0.247
8HLQ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Niraparib (MK-4827) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 3JD 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.70 Å R-free 0.282
8HLQ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Niraparib (MK-4827) Deposited 2022-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 2 3JD 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.70 Å R-free 0.282
8JNY Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrazolopyrimidine carboxamide inhibitor Deposited 2023-06-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L ERV 6-methylpyrazolo[1,5-a]pyrimidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 3.20 Å R-free 0.268
8JNY Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrazolopyrimidine carboxamide inhibitor Deposited 2023-06-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L ERV 6-methylpyrazolo[1,5-a]pyrimidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 3.20 Å R-free 0.268
9IM8 Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor Deposited 2024-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 A1D9M 5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.241
9IM8 Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor Deposited 2024-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L A1D9M 5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.241
9ZQ9 Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–212（123 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9ZQA Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–212（123 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9ZQB Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–583（494 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–583（494 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.37 Å

29 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PARP2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–363； UniProt 223–583

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 4zzy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zzy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zzy
Deposition date deposition_date2015-04-15
Structure title titleStructure of human PARP2 catalytic domain bound to an isoindolinone inhibitor
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.24 Å
Radius of gyration Rg (electron density) rg_electron21.03 Å
Forward intensity I(0) i027087900.00
Molecular weight molecular_weight40209.0 kDa
Excluded volume excluded_volume50543 ų
Envelope volume envelope_volume60993 ų
Hydration-shell volume shell_volume23915 ų
Envelope diameter envelope_diameter72.5 Å
Shell Rg shell_rg28.09 Å
Envelope Rg envelope_rg21.27 Å
Shape Rg shape_rg21.02 Å
Total Rg total_rg21.98 Å
Total atoms total_atoms2824
Residues n_residues351
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 dmax70.3 Å
Rg (real space) rg_real22.13 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real2.7090e+07
I(0) uncertainty (real space) i0_real_error3.4320e+05
Rg (reciprocal space) rg_reciprocal22.15 Å
I(0) (reciprocal space) i0_reciprocal27090000.0000
Solution quality estimate total_estimate0.9014
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.149
Kurtosis Kurtosis kurtosis-0.460
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5159000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4zzya1
Class classa — All alpha proteins
Fold Fold folda.41 — Domain of poly(ADP-ribose) polymerase
Superfamily Superfamily superfamilya.41.1 — Domain of poly(ADP-ribose) polymerase
Family Family familya.41.1.0 — automated matches
Domain ID domain_idd4zzya2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.166 — ADP-ribosylation
Superfamily Superfamily superfamilyd.166.1 — ADP-ribosylation
Family Family familyd.166.1.2 — Poly(ADP-ribose) polymerase, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id4zzyA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology142 — Poly(ADP-ribose) Polymerase; domain 1
Homologous superfamily homologous superfamily10 — Poly(ADP-ribose) polymerase, regulatory domain
Domain ID domain_id4zzyA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)