SMTL ID : 5mil.1

Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity islands transfer.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

DUP.1: 18 residues within 4Å: Chain A: Q.51, F.54, D.55, L.61, E.73, E.76, D.104, A.107, F.108, K.183, M.184, N.187 Chain B: N.79, E.82, K.85, W.87 Ligands: MG.2, MG.3 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.79, B:K.85, B:W.87, A:Q.51, A:D.55, A:N.187 Salt bridges: B:K.85 pi-Stacking: B:W.87, B:W.87 Hydrophobic interactions: A:A.107, A:F.108, A:F.108 Water bridges: A:D.104 DUP.4: 18 residues within 4Å: Chain A: N.79, K.85, W.87, K.93 Chain B: Q.51, F.54, D.55, L.61, E.73, E.76, D.104, A.107, F.108, K.183, M.184, N.187 Ligands: MG.5, MG.6 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:A.107, B:F.108 Hydrogen bonds: B:Q.51, B:D.55, B:E.73, B:E.76, B:K.183, B:N.187, A:N.79, A:K.85 Water bridges: B:S.111, B:N.187, A:E.82, A:K.93 Salt bridges: A:K.85, A:K.93 pi-Stacking: A:W.87, A:W.87

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.73, E.76, E.101, D.104 Ligands: DUP.1, MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.73, A:E.76, A:E.101, A:D.104, H2O.1 MG.3: 5 residues within 4Å: Chain A: E.73, E.76 Chain B: K.85 Ligands: DUP.1, MG.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.73, A:E.76, H2O.2 MG.5: 6 residues within 4Å: Chain B: E.73, E.76, E.101, D.104 Ligands: DUP.4, MG.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.73, B:E.76, B:E.101, B:D.104, H2O.2 MG.6: 5 residues within 4Å: Chain A: K.85 Chain B: E.73, E.76 Ligands: DUP.4, MG.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.73, B:E.76, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowring, J. et al., Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer. Elife (2017)

Release Date

2017-09-06

Peptides

DUTPase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DUTPase family protein

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