SMTL ID : 7b7v.1

Structure of NUDT15 in complex with Acyclovir monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 4DG: 2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl dihydrogen phosphate(Non-covalent)

4DG.1: 14 residues within 4Å: Chain A: G.15, R.34, Q.44, L.45, G.47, G.48, H.49, Y.92, T.94, K.116, F.135, W.136, G.137 Ligands: CL.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.45, A:G.137 Water bridges: A:R.34, A:R.34, A:R.34, A:R.34, A:R.34, A:H.49, A:K.116, A:K.116, A:K.116 Salt bridges: A:R.34, A:H.49, A:K.116 pi-Stacking: A:Y.92, A:F.135, A:W.136 4DG.5: 16 residues within 4Å: Chain B: G.15, R.34, S.37, Q.44, L.45, P.46, G.47, G.48, H.49, Y.92, T.94, K.116, F.135, W.136, G.137 Ligands: CL.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.37, B:G.47, B:T.94, B:G.137 Water bridges: B:R.34, B:R.34, B:R.34, B:R.34, B:R.34 Salt bridges: B:R.34, B:K.116 pi-Stacking: B:Y.92, B:F.135

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: G.47, E.67 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.47, A:E.67, H2O.2, H2O.3, H2O.3, H2O.3 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: G.47, E.67 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.47, B:E.67, H2O.6, H2O.7, H2O.8, H2O.8 MG.7: 2 residues within 4Å: Chain B: E.63, E.66 No protein-ligand interaction detected (PLIP)

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

CL.4: 6 residues within 4Å: Chain A: Q.44, L.45, F.135, G.137, L.138 Ligands: 4DG.1 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: Q.44, L.45, F.135, L.138 Ligands: 4DG.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishii, R. et al., NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir. Nat Commun (2021)

Release Date

2021-05-19

Peptides

Probable 8-oxo-dGTP diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable 8-oxo-dGTP diphosphatase NUDT15

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