SMTL ID : 7l9f.4 (3 other biounits)

Crystal structure of human ARH3 bound to calcium and ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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)

AR6.1: 24 residues within 4Å: Chain A: D.80, D.81, G.118, Y.119, G.120, A.121, G.122, V.123, F.146, K.149, G.150, S.151, Y.152, G.153, N.154, G.155, M.158, H.185, L.238, I.274, D.317, T.320 Ligands: CA.2, CA.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.118, A:G.120, A:A.121, A:G.122, A:V.123, A:G.150, A:S.151, A:Y.152, A:Y.152, A:G.153, A:N.154, A:G.155, A:T.320 Water bridges: A:S.151, A:G.155 Salt bridges: A:H.185, A:H.185 pi-Stacking: A:F.146, A:F.146, A:Y.152

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.317, D.319, T.320 Ligands: AR6.1, CA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.317, A:D.319, A:T.320, H2O.2 CA.3: 6 residues within 4Å: Chain A: T.79, D.80, D.81, D.319 Ligands: AR6.1, CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.79, A:D.80, A:D.81, A:D.319, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pourfarjam, Y. et al., Structural and biochemical analysis of human ADP-ribosyl-acceptor hydrolase 3 reveals the basis of metal selectivity and different roles for the two magnesium ions. J.Biol.Chem. (2021)

Release Date

2021-04-28

Peptides

Poly(ADP-ribose) glycohydrolase ARH3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Poly(ADP-ribose) glycohydrolase ARH3

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