SMTL ID : 9mbk.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

monomer

Ligands

1 x 6U4: [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

6U4.1: 19 residues within 4Å: Chain A: Y.7, T.8, L.9, N.33, G.36, G.37, K.38, E.52, F.72, F.74, M.81, V.83, W.117, D.119, D.120, W.123, F.139 Ligands: NA.2, NA.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.33, A:G.36, A:K.38, A:D.119, A:D.119 Water bridges: A:K.23, A:G.36, A:K.38, A:K.38, A:K.38, A:K.38, A:K.38, A:R.51 Salt bridges: A:K.38, A:K.38 pi-Stacking: A:W.117, A:W.117

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

NA.2: 2 residues within 4Å: Chain A: E.100 Ligands: 6U4.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.100 NA.3: 6 residues within 4Å: Chain A: G.37, K.38, Q.40, R.51, E.52 Ligands: 6U4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.38, A:E.52

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
A

7,8-dihydro-8-oxoguanine triphosphatase

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