SMTL ID : 5lpg.1

Structure of NUDT15 in complex with 6-thio-GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: G.47, E.63, E.67 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.2, H2O.3 MG.3: 6 residues within 4Å: Chain B: G.47, E.63, E.67 Ligands: MG.4, MG.5, MG.6 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.63, B:E.67, H2O.4, H2O.4, H2O.4, H2O.6 MG.4: 6 residues within 4Å: Chain B: G.47, G.48, E.63, E.67 Ligands: MG.3, MG.5 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.47, B:E.67, H2O.4, H2O.4, H2O.5, H2O.5 MG.5: 6 residues within 4Å: Chain B: G.48, H.49, E.63 Ligands: MG.3, MG.4, MG.6 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: R.62, E.63 Ligands: MG.3, MG.5 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.63, H2O.3, H2O.4, H2O.4, H2O.5, H2O.6

1 x 71V: [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-sulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

71V.2: 11 residues within 4Å: Chain A: R.34, Q.44, L.45, P.46, G.47, G.48, H.49, Y.90, F.135, G.137, L.138 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.45, A:P.46, A:H.49, A:G.137 Water bridges: A:R.34, A:R.34, A:E.63, A:Y.90 Salt bridges: A:H.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valerie, N.C. et al., NUDT15 Hydrolyzes 6-Thio-DeoxyGTP to Mediate the Anticancer Efficacy of 6-Thioguanine. Cancer Res. (2016)

Release Date

2016-08-24

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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