SMTL ID : 3zf6.1

Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase D81A D110C S168C mutant with dUpNHpp).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)(Non-functional Binders)

NI.1: 5 residues within 4Å: Chain A: D.129 Chain B: D.129 Chain C: D.129 Ligands: NI.4, NI.7 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.129, A:D.129, H2O.1, H2O.3, H2O.5 NI.3: 2 residues within 4Å: Ligands: NI.6, NI.9 No protein-ligand interaction detected (PLIP) NI.4: 5 residues within 4Å: Chain A: D.129 Chain B: D.129 Chain C: D.129 Ligands: NI.1, NI.7 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.129, A:D.129, H2O.1, H2O.3, H2O.5 NI.6: 2 residues within 4Å: Ligands: NI.3, NI.9 No protein-ligand interaction detected (PLIP) NI.7: 5 residues within 4Å: Chain A: D.129 Chain B: D.129 Chain C: D.129 Ligands: NI.1, NI.4 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.129, A:D.129, H2O.1, H2O.3, H2O.5 NI.9: 2 residues within 4Å: Ligands: NI.3, NI.6 No protein-ligand interaction detected (PLIP)

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

UMP.2: 15 residues within 4Å: Chain A: L.95, G.112, K.113, I.114, A.115, Y.118, N.121, L.122, G.123, N.125 Chain B: G.198, F.199 Chain C: R.98, S.99, Q.171 20 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: A:I.114, A:Y.118 Hydrogen bonds: A:K.113, A:A.115, A:Y.118, A:G.123, A:G.123, A:N.125, C:S.99, C:S.99, C:Q.171 Water bridges: A:G.112, A:K.113, A:K.113, A:N.125, B:G.198, B:S.201, C:R.98, C:G.100 pi-Stacking: B:F.199 UMP.5: 15 residues within 4Å: Chain A: R.98, S.99, Q.171 Chain B: L.95, G.112, K.113, I.114, A.115, Y.118, N.121, L.122, G.123, N.125 Chain C: G.198, F.199 19 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: B:I.114, B:Y.118 Hydrogen bonds: B:K.113, B:A.115, B:G.123, B:G.123, B:N.125, A:S.99, A:S.99, A:Q.171 Water bridges: B:G.112, B:K.113, B:K.113, B:N.125, C:G.198, A:R.98, A:S.99, A:G.100 pi-Stacking: C:F.199 UMP.8: 15 residues within 4Å: Chain A: G.198, F.199 Chain B: R.98, S.99, Q.171 Chain C: L.95, G.112, K.113, I.114, A.115, Y.118, N.121, L.122, G.123, N.125 19 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: C:I.114, C:Y.118 Hydrogen bonds: C:K.113, C:A.115, C:G.123, C:G.123, C:N.125, B:S.99, B:S.99, B:Q.171 Water bridges: C:G.112, C:K.113, C:K.113, C:N.125, B:R.98, B:G.100, A:G.198, A:S.201 pi-Stacking: A:F.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tormo-Mas, M.A. et al., Phage Dutpases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-Like Mechanism. Mol.Cell (2013)

Release Date

2013-01-30

Peptides

DUTPASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DUTPASE