SMTL ID : 8rsm.1

Crystal structure of Streptococcus pyogenes macrodomain in complex with ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION

ZN.1: 4 residues within 4Å: Chain A: C.116, H.121, C.123 Ligands: AR6.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.116, A:H.121, A:C.123

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

AR6.2: 25 residues within 4Å: Chain A: G.95, D.96, I.97, A.108, A.109, N.110, C.116, H.121, G.122, C.123, I.124, D.125, A.127, S.214, S.216, T.217, G.218, E.219, F.220, K.224, N.253, F.255, T.256, D.259 Ligands: ZN.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:D.96, A:I.97, A:N.110, A:I.124, A:D.125, A:S.216, A:T.217, A:G.218, A:E.219, A:F.220, A:K.224, A:K.224 Water bridges: A:R.98, A:D.125, A:S.214, A:S.214, A:S.214, A:F.255 Salt bridges: A:H.121 pi-Stacking: A:F.255, A:F.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ariza, A. et al., Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains. J.Biol.Chem. (2024)

Release Date

2024-09-25

Peptides

Protein-ADP-ribose hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein-ADP-ribose hydrolase