SMTL ID : 5otn.1

Crystal structure of zebrafish MTH1 in complex with O6-methyl-dGMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

monomer

Ligands

1 x 6OG: 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

6OG.1: 18 residues within 4Å: Chain A: T.11, L.12, K.26, F.30, N.36, G.39, G.40, K.41, F.75, F.77, M.84, E.103, W.120, D.122, D.123 Ligands: GOL.2, GOL.5, CA.11 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.11, A:N.36, A:N.36, A:G.39 Water bridges: A:G.39, A:K.41 Salt bridges: A:K.26, A:K.41, A:D.122, A:D.123 pi-Stacking: A:W.120, A:W.120

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: K.8, F.30, K.41, M.84 Ligands: 6OG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.41 Water bridges: A:E.82 GOL.3: 4 residues within 4Å: Chain A: L.9, V.42, Q.43, T.44 4 PLIP interactions: 4 interactions with chain A Water bridges: A:V.42, A:V.42, A:Q.43, A:G.45 GOL.4: 4 residues within 4Å: Chain A: P.128, L.129, Q.132, K.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.128, A:Q.132 GOL.5: 9 residues within 4Å: Chain A: K.26, R.28, G.29, F.30, E.103 Ligands: 6OG.1, CA.11, CA.13, CL.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.26, A:R.28, A:F.30 GOL.6: 7 residues within 4Å: Chain A: V.16, Q.17, P.18, G.19, L.131, K.133 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.17, A:G.19, A:K.133 GOL.7: 3 residues within 4Å: Chain A: Q.17, N.93, Y.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93, A:Y.94 GOL.8: 3 residues within 4Å: Chain A: A.121, I.124, L.125 No protein-ligand interaction detected (PLIP) GOL.9: 1 residues within 4Å: Chain A: S.117 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.116, A:M.119, A:A.121 GOL.10: 2 residues within 4Å: Chain A: K.134, E.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.155 Water bridges: A:E.155

3 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain A: G.39, E.59, E.103 Ligands: 6OG.1, GOL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.39, A:E.59, A:E.59, A:E.103, H2O.5 CA.12: 3 residues within 4Å: Chain A: E.55, E.58 Ligands: CA.13 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.55, A:E.55, A:E.58, H2O.2, H2O.4 CA.13: 3 residues within 4Å: Chain A: E.103 Ligands: GOL.5, CA.12 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.103, H2O.2

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

EDO.14: 4 residues within 4Å: Chain A: L.131, Q.132, K.133 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.132, A:K.133 EDO.15: 2 residues within 4Å: Chain A: S.117 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.117 EDO.16: 6 residues within 4Å: Chain A: I.114, P.115, F.116, S.117, Q.118 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.117, A:Q.118, A:Q.118

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.17: 3 residues within 4Å: Chain A: R.28, G.29 Ligands: GOL.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jemth, A.S. et al., MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP. Nucleic Acids Res. (2018)

Release Date

2018-09-05

Peptides

Nudix (Nucleoside diphosphate linked moiety X)-type motif 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nudix (Nucleoside diphosphate linked moiety X)-type motif 1