SMTL ID : 7s6h.2 (1 other biounit)

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

Coordinates

PDB Format Compare

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: R.38, F.64 Chain B: Y.54, R.71, W.73, K.84, L.101, K.105, F.122 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: 19 residues within 4Å: Chain A: K.35, S.36, R.38, A.39, S.40, R.54, M.63, F.64, V.68, P.69, H.70, W.71, 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

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: C.205, E.207, C.208, G.210, C.221, C.231, V.233 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.208, A:C.221, A:C.231 ZN.4: 4 residues within 4Å: Chain A: C.41, C.44, H.73, C.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.41, A:C.44, A:H.73, A:C.76

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

EDO.5: 5 residues within 4Å: Chain B: Y.311, N.388, H.391, T.392, F.491 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B: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.6: 22 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:Y.378, B:Y.378 Hydrogen bonds: B:H.344, B:G.345, B:G.345, B:S.346, B:N.350, B:G.358, B:R.360, B:R.360, B:S.386 pi-Stacking: B:Y.389, B:Y.389

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

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

Poly [ADP-ribose] polymerase 1

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