6NTU: Human PARP-1 ART domain

Crystal Structure of human PARP-1 ART domain bound to inhibitor UKTT-15. Determined by X-ray diffraction at 1.8 Å resolution. Released 5 Feb 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,125
Mol. weight: 31.42 kDa
Ligands: L1S
Released: 5 Feb 2020

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

Secondary structure: helices and β-sheets

6NTU contains 14 α-helices and 17 β-strands across 1 chain. 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: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	769-779	11
α-helix	790-796	7
β-strand	799-803	5	1
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	1
α-helix	844-848	5
α-helix	849-851	3
β-strand	857-864	8	1
α-helix	866-868	3
α-helix	869-875	7
β-strand	895-897	3	2
β-strand	898	1	1
α-helix	901-905	5
α-helix	906-908	3
β-strand	911	1	3
β-strand	914	1	3
β-strand	916-925	10	1
β-strand	929-932	4	2
α-helix	940-942	3
β-strand	947-950	4	2
β-strand	952-956	5	4
α-helix	958-960	3
β-strand	962-964	3	1
β-strand	967-969	3	1
α-helix	973	1
β-strand	974-976	3	4
β-strand	984-986	3	4
β-strand	988-991	4	2
α-helix	994-996	3
β-strand	997-1009	13	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 1	A	protein	271	Homo sapiens	P09874 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6NTU_1 Poly [ADP-ribose] polymerase 1 (chains A)
MGSSHHHHHHSSGLVPRGSHMTKSKLPKPVQDLIKMIFGSGSGSGGDPIDVNYEKLKTDI
KVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLW
HGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILL
GEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVND
TSLLYNEYIVYDIAQVNLKYLLKLKFNFKTS

Ligands and cofactors

ID	Name	Formula	Copies
L1S	methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1…	C25 H23 N7 O4	1

Water and common crystallization additives (SO4, 1PE, DMS) are not listed.

Primary citation

Structural basis for allosteric PARP-1 retention on DNA breaks. Zandarashvili, L., Langelier, M.F., Velagapudi, U.K. et al. Science (2020) 368. DOI 10.1126/science.aax6367 · 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)
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

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