SMTL ID : 7aom.1

Structure of NUDT15 in complex with Ganciclovir triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x RQ2: Ganciclovir triphosphate(Non-covalent)

RQ2.1: 17 residues within 4Å: Chain A: R.34, Q.44, L.45, P.46, G.47, G.48, H.49, E.63, E.67, Y.90, Y.92, T.94, K.116, F.135, G.137, L.138 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.34, A:L.45, A:L.45, A:L.45, A:H.49, A:E.63, A:G.137, A:L.138 Water bridges: A:G.47, A:G.47, A:R.62, A:K.116 Salt bridges: A:R.34, A:H.49, A:H.49, A:K.116 pi-Stacking: A:F.135, A:F.135 RQ2.3: 19 residues within 4Å: Chain B: G.15, V.16, R.34, Q.44, L.45, P.46, G.47, G.48, H.49, E.63, E.67, Y.90, Y.92, T.94, K.116, F.135, G.137, L.138 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.34, B:L.45, B:L.45, B:L.45, B:H.49, B:Y.90, B:T.94, B:G.137, B:L.138 Water bridges: B:G.47, B:G.47, B:H.49, B:R.62, B:Y.92 Salt bridges: B:R.34, B:H.49, B:H.49, B:K.116 pi-Stacking: B:F.135, B:F.135

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: R.34, G.47, E.67 Ligands: RQ2.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.47, A:E.67, H2O.1, H2O.4 MG.4: 4 residues within 4Å: Chain B: G.47, G.48, E.67 Ligands: RQ2.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.47, B:E.67, H2O.6, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S.M. et al., NUDT15-mediated hydrolysis limits the efficacy of anti-HCMV drug ganciclovir. Cell Chem Biol (2021)

Release Date

2021-06-02

Peptides

Nucleotide triphosphate diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleotide triphosphate diphosphatase NUDT15

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