6XVW: Catalytic domain of human PARP-1

Catalytic domain of human PARP-1 in complex with the inhibitor MC2050. Determined by X-ray diffraction at 2.0 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,908
Mol. weight: 81.03 kDa
Ligands: NI, O3H
Released: 3 Jun 2020

Explore 6XVW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XVW contains 46 α-helices and 38 β-strands across 2 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, 19 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	1
α-helix	703-722	20
α-helix	728-739	12
β-strand	742	1	1
α-helix	757-778	22
α-helix	789-796	8
β-strand	799-803	5	2
α-helix	804-805	2
α-helix	809-820	12
α-helix	823-825	3
β-strand	829-841	13	2
α-helix	844-848	5
α-helix	849-853	5
β-strand	857-864	8	2
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
α-helix	886-888	3
β-strand	895-897	3	3
β-strand	898	1	2
α-helix	901-904	4
α-helix	905-908	4
β-strand	911	1	4
β-strand	914	1	4
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	5
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	5
β-strand	984-986	3	5
β-strand	988-991	4	3
α-helix	994-996	3
β-strand	997-1009	13	2

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	6
α-helix	698-700	3
α-helix	703-718	16
α-helix	719-723	5
α-helix	728-739	12
β-strand	742	1	6
α-helix	757-779	23
α-helix	789-796	8
β-strand	799-803	5	7
α-helix	804-805	2
α-helix	809-820	12
α-helix	823-825	3
β-strand	829-841	13	7
α-helix	844-848	5
α-helix	849-853	5
β-strand	857-864	8	7
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
α-helix	886-888	3
β-strand	895-897	3	8
β-strand	898	1	7
α-helix	901-905	5
α-helix	906-908	3
β-strand	911	1	9
β-strand	914	1	9
β-strand	916-925	10	7
β-strand	929-932	4	8
α-helix	941-942	2
β-strand	947-950	4	8
α-helix	951	1
β-strand	952-956	5	10
α-helix	958-960	3
β-strand	962-964	3	7
β-strand	967-969	3	7
α-helix	972-973	2
β-strand	974-976	3	10
β-strand	984-986	3	10
β-strand	988-991	4	8
α-helix	994-996	3
β-strand	997-1009	13	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 1	A, B	protein	354	Homo sapiens	P09874 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6XVW_1 Poly [ADP-ribose] polymerase 1 (chains A, B)
HMSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAV
SQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRG
GSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIE
REGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADM
VSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSA
NISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTSLW

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	6
O3H	2-[2-(4-pyridin-2-ylpiperazin-1-yl)ethylsulfanyl]-3~{H}-quinazolin-4-one	C19 H21 N5 O S	2

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

Primary citation

From PARP1 to TNKS2 Inhibition: A Structure-Based Approach. Tomassi, S., Pfahler, J., Mautone, N. et al. ACS Med Chem Lett (2020) 11:862-868. DOI 10.1021/acsmedchemlett.9b00654 · 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
7KK5 1.7 Å, Structure of the catalytic domain of PARP1 in complex with niraparib
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…

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