SMTL ID : 7akr.1 (3 other biounits)

Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with ADP-ribose dimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: T.62, D.63, D.64, D.302 Ligands: MG.2, AR6.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.62, A:D.63, A:D.64, A:D.302, H2O.4 MG.2: 6 residues within 4Å: Chain A: D.300, D.302, T.303 Ligands: MG.1, AR6.3, AR6.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.300, A:D.302, A:T.303, H2O.5

2 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: 22 residues within 4Å: Chain A: D.63, D.64, 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, D.302, T.303 Ligands: MG.1, MG.2, AR6.12 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.63, A:G.103, A:G.103, A:A.104, A:G.105, A:V.106, A:G.133, A:S.134, A:Y.135, A:G.136, A:G.138, A:T.303 Water bridges: A:D.63 Salt bridges: A:H.168, A:H.168 pi-Stacking: A:F.129, A:F.129, A:Y.135 AR6.12: 6 residues within 4Å: Chain A: G.101, Y.102, G.103, I.257 Ligands: MG.2, AR6.3 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: M.223, E.224, R.231 Ligand excluded by PLIP

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: L.13, T.65, A.68, R.69, T.335 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.68, A:R.69, A:T.335 EDO.6: 4 residues within 4Å: Chain A: G.105, T.108, Q.128, F.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.108, A:Q.128, A:F.129 Water bridges: A:T.108, A:N.130 EDO.7: 4 residues within 4Å: Chain A: E.45, A.283, F.284, Q.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.288, A:Q.288 Water bridges: A:N.285 EDO.8: 3 residues within 4Å: Chain A: D.30, N.255, L.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.255, A:L.297 EDO.9: 3 residues within 4Å: Chain A: V.84, D.85, H.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.85 Water bridges: A:D.82, A:D.85 EDO.10: 3 residues within 4Å: Chain A: K.78, F.81, D.82 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.81 EDO.11: 2 residues within 4Å: Chain A: R.161, D.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.161 Water bridges: A:Q.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rack, J.G.M. et al., Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal. Nat Commun (2021)

Release Date

2021-06-16

Peptides

ADP-ribose glycohydrolase ARH3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

ADP-ribose glycohydrolase ARH3

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