SMTL ID : 5bon.2 (3 other biounits)

Crystal structure of human Nudt15 (MTH2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: G.47, G.48, E.67 Ligands: MG.3, MG.4 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.47, A:E.67, H2O.2, H2O.4, H2O.5, H2O.5 MG.2: 3 residues within 4Å: Chain A: E.63 Ligands: MG.3, MG.4 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.63, H2O.2, H2O.3, H2O.3, H2O.5, H2O.10 MG.3: 6 residues within 4Å: Chain A: G.47, E.63, E.67 Ligands: MG.1, MG.2, MG.4 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.63, A:E.67, H2O.2, H2O.3, H2O.4, H2O.5 MG.4: 4 residues within 4Å: Chain A: G.48 Ligands: MG.1, MG.2, MG.3 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: G.47, G.48, E.67 Ligands: MG.6, MG.8 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.47, B:E.67, H2O.7, H2O.7, H2O.9, H2O.9 MG.6: 6 residues within 4Å: Chain B: G.47, E.63, E.67 Ligands: MG.5, MG.7, MG.8 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.63, B:E.67, H2O.7, H2O.8, H2O.8, H2O.9 MG.7: 5 residues within 4Å: Chain B: H.49, R.62, E.63 Ligands: MG.6, MG.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.63, H2O.5, H2O.7, H2O.7, H2O.8, H2O.9 MG.8: 8 residues within 4Å: Chain B: G.47, G.48, H.49, E.63, E.67 Ligands: MG.5, MG.6, MG.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carter, M. et al., Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2. Nat Commun (2015)

Release Date

2015-08-05

Peptides

Probable 8-oxo-dGTP diphosphatase NUDT15: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Probable 8-oxo-dGTP diphosphatase NUDT15

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