SMTL ID : 8i1j.2 (1 other biounit)

Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP at pH 9.7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 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: 21 residues within 4Å: Chain A: Y.7, T.8, L.9, K.23, N.33, G.36, G.37, K.38, E.52, E.56, F.72, F.74, M.81, V.83, W.117, D.119, N.120, W.123, F.139 Ligands: NA.2, NA.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.23, A:N.33, A:G.36, A:K.38, A:D.119, A:D.119, A:N.120 Salt bridges: A:K.23, A:K.38, A:K.38 pi-Stacking: A:W.117, A:W.117

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

NA.2: 5 residues within 4Å: Chain A: G.36, G.37, E.52, E.56 Ligands: 6U4.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.56 NA.3: 6 residues within 4Å: Chain A: G.37, K.38, Q.40, R.51, E.52 Ligands: 6U4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.51, A:E.52 Water bridges: A:E.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, T. et al., Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. Febs Lett. (2023)

Release Date

2023-03-22

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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