SMTL ID : 7r0d.1

Structure of NUDT15 in complex with Geranyl monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x RDZ: Geranyl phosphate(Non-covalent)

RDZ.1: 13 residues within 4Å: Chain A: G.15, V.16, G.17, L.45, P.46, G.47, G.48, H.49, E.63, Y.92, T.94, G.137 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.92, A:T.94 Hydrogen bonds: A:H.49 Water bridges: A:E.51, A:K.116, A:K.116, A:K.116 Salt bridges: A:H.49 RDZ.3: 12 residues within 4Å: Chain B: G.15, V.16, G.17, L.45, P.46, G.47, G.48, H.49, E.63, Y.92, T.94 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.92, B:T.94 Hydrogen bonds: B:H.49, B:E.63 Water bridges: B:E.63, B:E.63, B:E.63, B:E.63, B:E.67, B:K.116 Salt bridges: B:H.49

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.47, E.63, E.67 Ligands: RDZ.1 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.63, A:E.67, H2O.1, H2O.1, H2O.1, H2O.3 MG.4: 4 residues within 4Å: Chain B: G.47, E.63, E.67 Ligands: RDZ.3 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.63, B:E.67, H2O.4, H2O.5, H2O.5, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scaletti, E.R. et al., Kinetic and structural characterization of NUDT15 and NUDT18 as catalysts of isoprene pyrophosphate hydrolysis. Febs J. (2024)

Release Date

2023-11-29

Peptides

Probable 8-oxo-dGTP diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Probable 8-oxo-dGTP diphosphatase NUDT15

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