SMTL ID : 5zqy.1

Crystal structure of a poly(ADP-ribose) glycohydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: E.27, D.300, D.302, T.303 Ligands: MG.2, AR6.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.300, A:D.302, A:T.303, H2O.1, H2O.5 MG.2: 6 residues within 4Å: Chain A: T.62, D.63, D.64, D.302 Ligands: MG.1, AR6.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.62, A:D.63, A:D.64, H2O.1, H2O.6

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.3: 19 residues within 4Å: Chain A: D.63, G.101, G.103, A.104, G.105, V.106, F.129, G.133, S.134, Y.135, G.136, N.137, G.138, H.168, I.257, D.300, T.303 Ligands: MG.1, MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.101, A:A.104, A:G.105, A:V.106, A:G.133, A:S.134, A:Y.135, A:N.137, A:G.138 Water bridges: A:E.27, A:E.27, A:T.62, A:D.63, A:D.63, A:G.103, A:S.134, A:Y.135, A:D.300, A:T.303 Salt bridges: A:H.168, A:H.168 pi-Stacking: A:F.129, A:F.129, A:Y.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, M. et al., Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation. J. Biol. Chem. (2018)

Release Date

2018-08-15

Peptides

Poly(ADP-ribose) glycohydrolase ARH3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly(ADP-ribose) glycohydrolase ARH3