SMTL ID : 9mbg.2 (1 other biounit)

8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the ES complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.1: 18 residues within 4Å: Chain A: Y.7, T.8, L.9, K.23, R.25, N.33, G.36, G.37, K.38, F.72, M.81, V.83, W.117, D.119, D.120, W.123 Ligands: NA.2, NA.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.33, A:N.33, A:G.36, A:K.38 Salt bridges: A:K.23, A:K.23, A:K.23, A:K.38, A:K.38, A:D.119, A:D.120 pi-Stacking: A:W.117, A:W.117

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: K.23, G.36, G.37, E.56 Ligands: 8DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.23, A:E.56 NA.3: 5 residues within 4Å: Chain A: G.37, K.38, R.51, E.52 Ligands: 8DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.52 Water bridges: A:R.51, A:E.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirata, K. et al., Neutron and time-resolved X-ray crystallography reveal the substrate recognition and catalytic mechanism of human Nudix hydrolase MTH1. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-07-30

Peptides

7,8-dihydro-8-oxoguanine triphosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

7,8-dihydro-8-oxoguanine triphosphatase

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