SMTL ID : 5cco.1

Staphylococcus bacteriophage 80alpha dUTPase with dUMP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-trimer

Ligands

3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 15 residues within 4Å: Chain A: G.78, K.79, I.80, D.81, Y.84, N.87, L.88, G.89, N.91 Chain B: R.160, G.164, F.165, G.166 Chain C: R.64, S.65 20 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: A:I.80, A:Y.84, B:F.165 Hydrogen bonds: A:K.79, A:D.81, A:G.89, A:G.89, B:F.165, B:G.166, C:S.65, C:S.65, C:S.65 Water bridges: A:N.91, A:N.91, B:R.160, B:R.160, C:R.64, C:R.64 Salt bridges: B:R.160, C:R.64 UMP.4: 15 residues within 4Å: Chain A: R.64, S.65 Chain B: G.78, K.79, I.80, D.81, Y.84, N.87, L.88, G.89, N.91 Chain C: R.160, G.164, F.165, G.166 21 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: B:I.80, B:Y.84, C:F.165 Hydrogen bonds: B:K.79, B:D.81, B:Y.84, B:G.89, B:G.89, C:F.165, C:G.166, A:S.65, A:S.65, A:S.65 Water bridges: B:N.91, B:N.91, C:R.160, C:R.160, A:R.64, A:R.64 Salt bridges: C:R.160, A:R.64 UMP.7: 15 residues within 4Å: Chain A: R.160, G.164, F.165, G.166 Chain B: R.64, S.65 Chain C: G.78, K.79, I.80, D.81, Y.84, N.87, L.88, G.89, N.91 21 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: C:I.80, C:Y.84, A:F.165 Hydrogen bonds: C:K.79, C:D.81, C:Y.84, C:G.89, C:G.89, B:S.65, B:S.65, B:S.65, A:F.165, A:G.166 Water bridges: C:N.91, C:N.91, B:R.64, B:R.64, A:R.160, A:R.160 Salt bridges: B:R.64, A:R.160

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.77 Chain B: T.77 Chain C: T.77 Ligands: MG.5, MG.8 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: D.95 Chain B: D.95 Chain C: D.95 Ligands: MG.6, MG.9 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.95, A:D.95, B:D.95, H2O.1, H2O.6 MG.5: 5 residues within 4Å: Chain A: T.77 Chain B: T.77 Chain C: T.77 Ligands: MG.2, MG.8 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: D.95 Chain B: D.95 Chain C: D.95 Ligands: MG.3, MG.9 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.95, A:D.95, B:D.95, H2O.1, H2O.4 MG.8: 5 residues within 4Å: Chain A: T.77 Chain B: T.77 Chain C: T.77 Ligands: MG.2, MG.5 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain A: D.95 Chain B: D.95 Chain C: D.95 Ligands: MG.3, MG.6 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.95, A:D.95, B:D.95, H2O.4, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maiques, E. et al., Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party. Nucleic Acids Res. (2016)

Release Date

2016-05-11

Peptides

DUTPase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DUTPase