SMTL ID : 7arw.1 (1 other biounit)

Structure of human ARH3 E41A bound to alpha-NAD+ and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 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, 8NA.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.2 MG.2: 6 residues within 4Å: Chain A: D.64, D.300, D.302, T.303 Ligands: MG.1, 8NA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.300, A:D.302, A:T.303

1 x 8NA: alpha-Diphosphopyridine nucleotide(Non-covalent)

8NA.3: 21 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, G.299, D.300, T.303 Ligands: MG.1, MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.64, A:G.103, A:A.104, A:G.105, A:V.106, A:G.133, A:S.134, A:S.134, A:Y.135, A:G.136, A:N.137, A:N.137, A:G.138, A:G.299 Water bridges: A:T.62, A:Y.135, A:T.301 Salt bridges: A:H.168, A:H.168 pi-Stacking: A:F.129, A:F.129, A:Y.135

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

EDO.4: 2 residues within 4Å: Chain A: F.122, Q.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.126, A:Q.165 EDO.5: 5 residues within 4Å: Chain A: L.13, T.65, A.68, R.69, T.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.335 Water bridges: A:A.68 EDO.6: 5 residues within 4Å: Chain A: A.66, R.69, A.70, Q.73, E.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.66, A:R.69, A:A.70, A:Q.73 EDO.8: 5 residues within 4Å: Chain A: R.126, G.131, K.132, G.133, A.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.126 EDO.9: 4 residues within 4Å: Chain A: G.105, T.108, Q.128, F.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.108, A:F.129 Water bridges: A:T.108, A:N.130 EDO.10: 3 residues within 4Å: Chain A: R.272, P.276, P.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.272

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: E.57, G.331, Y.332, E.333, E.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.331, A:E.333, A:E.333, A:E.334

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
A

ADP-ribose glycohydrolase ARH3

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