SMTL ID : 7s6h.1 (1 other biounit)

Human PARP1 deltaV687-E688 bound to NAD+ analog EB-47 and to a DNA double strand break.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DC- DG- DA- DC- DG: DNA (5'-D(*CP*GP*AP*CP*G)-3')(Non-covalent)

DC-DG-DA-DC-DG.1: 14 residues within 4Å: Chain A: Y.54, R.71, W.73, K.84, L.101, K.105, F.122 Chain B: R.38, F.64 Ligands: DC-DG-DT-DC-DG.2, DC-DG-DT-DC-DG.2, DC-DG-DT-DC-DG.2, DC-DG-DT-DC-DG.2, DC-DG-DT-DC-DG.2 Protein-ligand interaction information (PLIP) not available

1 x DC- DG- DT- DC- DG: DNA (5'-D(*CP*GP*TP*CP*G)-3')(Non-covalent)

DC-DG-DT-DC-DG.2: 20 residues within 4Å: Chain B: K.35, S.36, R.38, A.39, S.40, R.54, M.63, F.64, V.68, P.69, H.70, W.71, K.172, S.184, G.185 Ligands: DC-DG-DA-DC-DG.1, DC-DG-DA-DC-DG.1, DC-DG-DA-DC-DG.1, DC-DG-DA-DC-DG.1, DC-DG-DA-DC-DG.1 Protein-ligand interaction information (PLIP) not available

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: Y.311, N.388, H.391, T.392, F.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.392

1 x 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(Non-covalent)

UHB.4: 22 residues within 4Å: Chain A: W.343, H.344, G.345, S.346, N.350, G.353, I.354, Q.357, G.358, L.359, R.360, A.362, T.369, Y.371, G.376, Y.378, F.379, A.380, K.385, S.386, Y.389, E.470 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.378, A:Y.378 Hydrogen bonds: A:H.344, A:G.345, A:G.345, A:S.346, A:N.350, A:G.358, A:R.360, A:R.360, A:S.386 pi-Stacking: A:Y.389, A:Y.389

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 7 residues within 4Å: Chain B: C.205, E.207, C.208, G.210, C.221, C.231, V.233 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.205, B:C.208, B:C.221, B:C.231 ZN.6: 5 residues within 4Å: Chain B: C.41, K.43, C.44, H.73, C.76 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.41, B:C.44, B:H.73, B:C.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rouleau-Turcotte, E. et al., Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery. Mol.Cell (2022)

Release Date

2022-06-29

Peptides

Poly [ADP-ribose] polymerase 1: A
Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Poly [ADP-ribose] polymerase 1

Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)

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