SMTL ID : 6vkq.4 (3 other biounits)

Crystal Structure of human PARP-1 CAT domain bound to inhibitor EB-47

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

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.1: 19 residues within 4Å: Chain A: D.127, L.130, D.131, H.223, G.224, S.225, N.229, I.233, Q.236, G.237, L.238, R.239, G.249, Y.250, Y.257, F.258, S.265, Y.268, E.349 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.268 Hydrogen bonds: A:H.223, A:G.224, A:S.225, A:N.229, A:G.237, A:R.239, A:Y.268 pi-Stacking: A:Y.268

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: H.187, K.264, L.345, L.346, Y.347, E.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.346, A:Y.347, A:Y.347 Salt bridges: A:K.264 SO4.3: 3 residues within 4Å: Chain A: R.219, M.290, K.310 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.219, A:K.310 SO4.4: 2 residues within 4Å: Chain A: Q.207, K.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.207 Salt bridges: A:K.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zandarashvili, L. et al., Structural basis for allosteric PARP-1 retention on DNA breaks. Science (2020)

Release Date

2020-06-17

Peptides

Poly [ADP-ribose] polymerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Poly [ADP-ribose] polymerase 1

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