SMTL ID : 3ac9.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 8GD: 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)(Non-covalent)

8GD.1: 7 residues within 4Å: Chain A: W.15, V.16, R.38, L.85 Chain B: T.32, W.33, E.34 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.85 Hydrogen bonds: A:R.38, A:R.38, B:E.34, B:E.34, B:E.34 pi-Stacking: A:W.15, A:W.15, A:W.15, A:W.15, B:W.33, B:W.33, B:W.33 pi-Cation interactions: B:W.33 8GD.2: 15 residues within 4Å: Chain A: W.33, E.34, G.122 Chain B: W.15, V.16, R.38, R.71, A.83, G.84, L.85, E.99, E.103, E.153 Ligands: MN.3, MN.4 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.38, B:L.85, B:E.153, A:E.34, A:E.34, A:E.34 Water bridges: B:W.15, B:Q.69, B:R.71, B:A.83 Salt bridges: B:R.71 pi-Stacking: B:W.15, B:W.15, B:W.15, A:W.33, A:W.33, A:W.33

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

MN.3: 6 residues within 4Å: Chain B: A.83, E.99, E.103, E.153 Ligands: 8GD.2, MN.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.99, B:E.103, H2O.7 MN.4: 5 residues within 4Å: Chain B: R.71, A.83, E.103 Ligands: 8GD.2, MN.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.83, B:E.103, H2O.6, H2O.6

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

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