7KK5: Catalytic domain of PARP1

Structure of the catalytic domain of PARP1 in complex with niraparib. Determined by X-ray diffraction at 1.7 Å resolution. Released 6 Jan 2021.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,827
Mol. weight: 160.47 kDa
Ligands: 3JD
Released: 6 Jan 2021

Explore 7KK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KK5 contains 83 α-helices and 70 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	1
α-helix	698-700	3
α-helix	703-721	19
α-helix	727-739	13
β-strand	742	1	1
α-helix	749-751	3
α-helix	755-779	25
α-helix	789-796	8
β-strand	799-803	5	2
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	2
α-helix	844-848	5
α-helix	849-851	3
β-strand	857-864	8	2
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
β-strand	895-897	3	3
β-strand	898	1	2
α-helix	901-905	5
α-helix	906-908	3
β-strand	916-925	10	2
β-strand	929-932	4	3
α-helix	941-942	2
β-strand	947-950	4	3
α-helix	951	1
β-strand	952-956	5	4
α-helix	958-960	3
β-strand	962-964	3	2
β-strand	967-969	3	2
α-helix	972-973	2
β-strand	974-976	3	4
β-strand	984-986	3	4
β-strand	988-991	4	3
α-helix	994-996	3
β-strand	997-1009	13	2

Chain B: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	5
α-helix	698-700	3
α-helix	703-722	20
α-helix	726-739	14
β-strand	742	1	5
α-helix	748-751	4
α-helix	755-779	25
α-helix	789-796	8
β-strand	799-803	5	6
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	6
α-helix	844-848	5
α-helix	849-853	5
β-strand	857-863	7	6
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
β-strand	895-897	3	7
β-strand	898	1	6
α-helix	901-905	5
α-helix	906-908	3
β-strand	911	1	8
β-strand	914	1	8
β-strand	916-925	10	6
β-strand	929-932	4	7
α-helix	940-942	3
β-strand	947-950	4	7
β-strand	952-956	5	9
α-helix	958-960	3
β-strand	962-964	3	6
β-strand	967-969	3	6
α-helix	972-973	2
β-strand	974-976	3	9
β-strand	984-986	3	9
β-strand	988-991	4	7
α-helix	994-996	3
β-strand	997-1009	13	6

Chain C: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	10
α-helix	698-700	3
α-helix	703-722	20
α-helix	726-739	14
β-strand	742	1	10
α-helix	755-779	25
α-helix	789-796	8
β-strand	799-803	5	11
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	11
α-helix	844-852	9
β-strand	857-863	7	11
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
β-strand	895-897	3	12
β-strand	898	1	11
α-helix	901-905	5
α-helix	906-908	3
β-strand	916-925	10	11
β-strand	929-932	4	12
β-strand	947-950	4	12
α-helix	951	1
β-strand	952-956	5	13
α-helix	958-960	3
β-strand	962-964	3	11
β-strand	967-969	3	11
α-helix	973	1
β-strand	974-976	3	13
β-strand	984-986	3	13
β-strand	988-991	4	12
α-helix	994-996	3
β-strand	997-1009	13	11

Chain D: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	14
α-helix	698-700	3
α-helix	703-719	17
α-helix	729-739	11
β-strand	742	1	14
α-helix	755-779	25
α-helix	789-795	7
β-strand	799-803	5	15
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	15
α-helix	844-848	5
α-helix	849-851	3
β-strand	857-864	8	15
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
β-strand	895-897	3	16
β-strand	898	1	15
α-helix	901-905	5
α-helix	906-908	3
β-strand	916-925	10	15
β-strand	929-932	4	16
α-helix	941-942	2
β-strand	947-950	4	16
α-helix	951	1
β-strand	952-956	5	17
α-helix	958-960	3
β-strand	962-964	3	15
β-strand	967-969	3	15
α-helix	973	1
β-strand	974-976	3	17
β-strand	984-986	3	17
β-strand	988-991	4	16
α-helix	994-996	3
β-strand	997-1009	13	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 1	A, B, C, D	protein	352	Homo sapiens	P09874 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7KK5_1 Poly [ADP-ribose] polymerase 1 (chains A, B, C, D)
GSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQA
VSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLR
GGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKI
EREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFAD
MVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPS
ANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT

Ligands and cofactors

ID	Name	Formula	Copies
3JD	2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide	C19 H20 N4 O	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Dissecting the molecular determinants of clinical PARP1 inhibitor selectivity for tankyrase1. Ryan, K., Bolanos, B., Smith, M. et al. J Biol Chem (2021) 296:100251-100251. DOI 10.1074/jbc.RA120.016573 · PubMed

Other PDB entries of the same protein (UniProt P09874 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NRH 1.5 Å, Crystal Structure of human PARP-1 ART domain bound inhibitor UTT63
9ETQ 1.59 Å, Crystal structure of PARP1 catalytic domain bound to AZD5305 (SARUPARIB)
7AAC 1.59 Å, Crystal structure of the catalytic domain of human PARP1 in complex with veliparib
6NRJ 1.65 Å, Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT93
7KK2 1.7 Å, Structure of the catalytic domain of PARP1
2RIQ 1.7 Å, Crystal Structure of the Third Zinc-binding domain of human PARP-1
6NRG 1.7 Å, Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT57
7AAA 1.74 Å, Crystal structure of the catalytic domain of human PARP1 (apo)
6NTU 1.8 Å, Crystal Structure of human PARP-1 ART domain bound to inhibitor UKTT-15
9ETR 1.82 Å, Crystal structure of PARP1 catalytic domain bound to AZD9574
7ONT 1.85 Å, PARP1 catalytic domain in complex with a selective pyridine carboxamide-based inhibitor…
4ZZZ 1.9 Å, Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor

Browse structure collections

About this viewer

MolViewer shows 7KK5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.