SMTL ID : 3zf4.1

Phage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y81A mutant with dUpNHpp).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-trimer

Ligands

3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 19 residues within 4Å: Chain A: L.95, G.112, K.113, I.114, D.115, A.118, N.121, L.122, G.123 Chain B: F.199, G.200, S.201, S.202 Chain C: N.54, R.98, S.99, G.100, Q.171 Ligands: MG.2 16 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: A:I.114 Hydrogen bonds: A:D.115, A:D.115, A:G.123, A:G.123, A:N.125, B:F.199, B:G.200, B:S.201, B:S.202, C:S.99, C:S.99, C:S.99, C:G.100, C:Q.171 Salt bridges: C:R.98 DUP.5: 19 residues within 4Å: Chain A: N.54, R.98, S.99, G.100, Q.171 Chain B: L.95, G.112, K.113, I.114, D.115, A.118, N.121, L.122, G.123 Chain C: F.199, G.200, S.201, S.202 Ligands: MG.6 16 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: C:F.199, C:G.200, C:S.201, C:S.202, B:D.115, B:D.115, B:G.123, B:G.123, B:N.125, A:S.99, A:S.99, A:S.99, A:G.100, A:Q.171 Hydrophobic interactions: B:I.114 Salt bridges: A:R.98 DUP.9: 19 residues within 4Å: Chain A: F.199, G.200, S.201, S.202 Chain B: N.54, R.98, S.99, G.100, Q.171 Chain C: L.95, G.112, K.113, I.114, D.115, A.118, N.121, L.122, G.123 Ligands: MG.10 15 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:S.99, B:S.99, B:S.99, B:G.100, B:Q.171, C:D.115, C:G.123, C:G.123, C:N.125, A:F.199, A:G.200, A:S.201, A:S.202 Salt bridges: B:R.98 Hydrophobic interactions: C:I.114

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: D.62, Q.171 Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: D.62, Q.171 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: D.62, Q.171 Ligands: DUP.9 No protein-ligand interaction detected (PLIP)

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

NI.3: 8 residues within 4Å: Chain A: Q.74, D.129 Chain B: Q.74, D.129 Chain C: Q.74, D.129 Ligands: NI.7, NI.11 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:D.129, B:D.129, C:D.129 NI.4: 2 residues within 4Å: Ligands: NI.8, NI.12 No protein-ligand interaction detected (PLIP) NI.7: 8 residues within 4Å: Chain A: Q.74, D.129 Chain B: Q.74, D.129 Chain C: Q.74, D.129 Ligands: NI.3, NI.11 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:D.129, B:D.129, C:D.129 NI.8: 2 residues within 4Å: Ligands: NI.4, NI.12 No protein-ligand interaction detected (PLIP) NI.11: 8 residues within 4Å: Chain A: Q.74, D.129 Chain B: Q.74, D.129 Chain C: Q.74, D.129 Ligands: NI.3, NI.7 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:D.129, B:D.129, C:D.129 NI.12: 2 residues within 4Å: Ligands: NI.4, NI.8 No protein-ligand interaction detected (PLIP)

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