SMTL ID : 6ntu.1

Crystal Structure of human PARP-1 ART domain bound to inhibitor UKTT-15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 10 residues within 4Å: Chain A: F.110, L.200, P.201, K.202, G.203, K.204, H.205, Y.251, D.252, Q.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.252, A:G.203, A:K.204, A:K.204 Water bridges: A:Q.255, A:P.201

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: H.121, G.153, I.154, Y.155 Ligands: L1S.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.155 DMS.3: 10 residues within 4Å: Chain A: F.150, Y.189, L.191, S.195, I.197, S.198, K.199, L.200, V.207, Y.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.195

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 3 residues within 4Å: Chain A: R.124, N.127, H.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.124

1 x L1S: methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate(Non-covalent)

L1S.5: 14 residues within 4Å: Chain A: W.120, H.121, G.122, T.146, G.147, Y.148, Y.155, F.156, A.157, K.162, S.163, Y.166, E.247 Ligands: DMS.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.146, A:Y.148, A:Y.155, A:A.157, A:Y.166, A:Y.166 Hydrogen bonds: A:G.122, A:G.122 Water bridges: A:Y.148 pi-Stacking: A:Y.166

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

SO4.6: 4 residues within 4Å: Chain A: K.162, L.243, L.244, Y.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.244, A:Y.245 Water bridges: A:K.162 Salt bridges: A:K.162 SO4.7: 4 residues within 4Å: Chain A: R.117, M.188, E.190, K.208 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.117, A:K.208

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

2020-02-05

Peptides

Poly [ADP-ribose] polymerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly [ADP-ribose] polymerase 1

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