SMTL ID : 8g0h.2 (1 other biounit)

Human PARP1 deltaV687-E688 bound to UKTT5 (compound 10) and to a DNA double strand break.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 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: 13 residues within 4Å: Chain A: Y.54, R.71, W.73, K.84, 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: 19 residues within 4Å: Chain B: K.35, S.36, R.38, A.39, S.40, K.42, R.54, M.63, F.64, V.68, P.69, 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

1 x YH0: 2-(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)-1H-benzimidazole-7-carboxamide(Non-covalent)

YH0.3: 18 residues within 4Å: Chain A: Y.192, L.195, S.196, Q.199, Q.241, A.244, W.343, H.344, G.345, P.367, G.370, Y.371, Y.378, F.379, A.380, K.385, Y.389, E.470 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.192, A:L.195, A:Q.199, A:A.244, A:P.367, A:Y.371, A:Y.371, A:Y.378, A:Y.378, A:A.380, A:K.385, A:E.470 Hydrogen bonds: A:Y.192, A:H.344, A:G.345, A:G.345 pi-Stacking: A:Y.389, A:Y.389

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: C.41, 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 ZN.5: 5 residues within 4Å: Chain B: C.205, C.208, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Velagapudi, U.K. et al., Novel modifications of PARP inhibitor veliparib increase PARP1 binding to DNA breaks. Biochem.J. (2024)

Release Date

2024-02-07

Peptides

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

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