SMTL ID : 6ijy.1 (1 other biounit)

Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 8-oxo-dGTP determined using a crystal obtained under microgravity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

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

8DG.1: 22 residues within 4Å: Chain A: Y.7, T.8, L.9, K.23, R.25, F.27, N.33, G.36, G.37, K.38, E.52, E.56, F.72, M.81, V.83, W.117, D.119, D.120, W.123, F.139 Ligands: NA.2, NA.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.83 Hydrogen bonds: A:N.33, A:N.33, A:G.36, A:K.38 Water bridges: A:K.23, A:K.23, A:R.25, A:F.27, A:E.56, A:E.100 Salt bridges: A:K.23, A:R.25, A:K.38, A:K.38, A:K.38, A:D.119, A:D.120 pi-Stacking: A:W.117, A:W.117

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

NA.2: 7 residues within 4Å: Chain A: K.23, G.36, G.37, E.56, E.100 Ligands: 8DG.1, NA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.23, A:G.36 NA.3: 4 residues within 4Å: Chain A: F.113, K.114, M.116, P.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.116, A:W.117 NA.4: 7 residues within 4Å: Chain A: G.36, G.37, E.52, E.56, E.100 Ligands: 8DG.1, NA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.52, A:E.56

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.2, E.73, V.75, G.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.2, A:E.73, A:G.76 GOL.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, T. et al., X-ray Structure Analysis of Human Oxidized Nucleotide Hydrolase MTH1 using Crystals Obtained under Microgravity. Int. J. Microgravity Sci. Appl. (2019)

Release Date

2019-02-20

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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