SMTL ID : 3aca.1

Crystal structure of human NUDT5 complexed with 8-oxo-dADP and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

5 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: A.84, E.100, E.104 Ligands: MN.2, 8DD.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.84, A:E.104, H2O.4, H2O.4 MN.2: 6 residues within 4Å: Chain A: A.84, E.100, E.104, E.154 Ligands: MN.1, 8DD.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.100, A:E.104, H2O.2, H2O.2 MN.3: 3 residues within 4Å: Chain A: R.99, E.100 Ligands: 8DD.4 No protein-ligand interaction detected (PLIP) MN.5: 4 residues within 4Å: Chain B: A.84, E.104 Ligands: MN.6, 8DD.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.84, B:E.104, H2O.9, H2O.9 MN.6: 6 residues within 4Å: Chain B: A.84, E.100, E.104, E.154 Ligands: MN.5, 8DD.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.100, B:E.104, H2O.6, H2O.8

2 x 8DD: 8-oxo-7,8-dihydro-2'-deoxy-adenosine-5'-diphosphate(Non-covalent)

8DD.4: 13 residues within 4Å: Chain A: W.16, R.39, R.72, A.84, G.85, L.86, E.100 Chain B: T.33, W.34, E.35 Ligands: MN.1, MN.2, MN.3 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.86 Hydrogen bonds: A:R.39, A:R.39, A:L.86, A:E.100, B:T.33, B:E.35 Water bridges: A:Q.70, A:A.84 Salt bridges: A:R.72 pi-Stacking: A:W.16, A:W.16, A:W.16, B:W.34, B:W.34, B:W.34 8DD.7: 14 residues within 4Å: Chain A: T.33, W.34, E.35, G.123 Chain B: W.16, R.39, R.72, A.84, G.85, L.86, E.104, E.154 Ligands: MN.5, MN.6 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.39, B:R.39, B:A.84, B:L.86, B:E.104, B:E.154, B:E.154, A:T.33, A:E.35 Water bridges: B:R.72, B:R.72, B:A.84 Salt bridges: B:R.72 pi-Stacking: B:W.16, B:W.16, B:W.16, A:W.34, A:W.34, A:W.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arimori, T. et al., Diverse substrate recognition and hydrolysis mechanisms of human NUDT5. Nucleic Acids Res. (2011)

Release Date

2011-01-12

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase