SMTL ID : 6fl4.1

A. thaliana NUDT1 in complex with 8-oxo-dGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: G.40, E.60 Ligands: MG.2, 8DG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.40, A:E.60, H2O.2, H2O.4 MG.2: 5 residues within 4Å: Chain A: G.40, E.56, E.60 Ligands: MG.1, 8DG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.56, A:E.60, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: G.40, E.56, E.60 Ligands: MG.5, 8DG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.56, B:E.60, H2O.6, H2O.6 MG.5: 4 residues within 4Å: Chain B: G.40, E.60 Ligands: MG.4, 8DG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.40, B:E.60, H2O.7, H2O.8

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

8DG.3: 21 residues within 4Å: Chain A: A.11, V.13, R.27, I.31, A.37, L.38, G.40, G.41, H.42, E.56, E.59, E.60, N.76, F.78, Y.87, S.89, K.110, F.127, P.129 Ligands: MG.1, MG.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.78, A:F.127 Hydrogen bonds: A:R.27, A:R.27, A:L.38, A:L.38, A:H.42, A:N.76, A:S.89 Water bridges: A:S.29, A:S.29, A:S.29, A:S.29, A:G.40, A:R.55, A:E.56, A:E.60, A:E.60, A:K.110 Salt bridges: A:R.27, A:H.42, A:H.42, A:H.42, A:K.110, A:K.110 pi-Stacking: A:F.127 8DG.6: 18 residues within 4Å: Chain B: A.11, V.13, R.27, A.37, L.38, G.40, G.41, H.42, E.56, E.60, N.76, Y.87, S.89, K.110, F.127, P.129 Ligands: MG.4, MG.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.87, B:F.127 Hydrogen bonds: B:R.27, B:R.27, B:L.38, B:L.38, B:H.42, B:S.89 Water bridges: B:G.40, B:R.55, B:R.55, B:E.56, B:E.59, B:K.110, B:K.110 Salt bridges: B:R.27, B:H.42, B:H.42, B:H.42, B:K.110, B:K.110 pi-Stacking: B:F.127, B:F.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jemth, A.S. et al., Crystal Structure and Substrate Specificity of the 8-oxo-dGTP Hydrolase NUDT1 from Arabidopsis thaliana. Biochemistry (2019)

Release Date

2019-02-06

Peptides

Nudix hydrolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nudix hydrolase 1