SMTL ID : 7esq.1

Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.151 Ligands: PPV.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.151, H2O.1, H2O.1, H2O.2 MG.5: 2 residues within 4Å: Chain B: S.151 Ligands: PPV.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.151, H2O.6, H2O.6, H2O.7 MG.9: 2 residues within 4Å: Chain C: S.151 Ligands: PPV.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.151, H2O.11, H2O.11, H2O.11 MG.13: 2 residues within 4Å: Chain D: S.151 Ligands: PPV.14 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.151, H2O.15, H2O.16, H2O.17 MG.17: 2 residues within 4Å: Chain E: S.151 Ligands: PPV.18 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.151, H2O.21, H2O.21, H2O.21 MG.21: 2 residues within 4Å: Chain F: S.151 Ligands: PPV.22 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.151, H2O.25, H2O.25, H2O.26

6 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 11 residues within 4Å: Chain A: G.145, T.146, G.147, A.148, G.149, K.150, S.151, E.167, N.249 Chain B: A.266 Ligands: MG.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.147, A:A.148, A:G.149, A:K.150, A:S.151, A:N.249 Water bridges: A:S.151, A:S.151, A:S.151, A:S.152, A:E.167, A:E.167, B:R.290, B:R.290 Salt bridges: A:K.150, A:K.150 PPV.6: 11 residues within 4Å: Chain B: G.145, T.146, G.147, A.148, G.149, K.150, S.151, E.167, N.249 Chain E: A.266 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.147, B:A.148, B:G.149, B:K.150, B:S.151, B:N.249 Water bridges: B:S.151, B:S.151, B:S.151, B:S.152, B:E.167, B:E.167, B:R.207 Salt bridges: B:K.150, B:K.150 PPV.10: 11 residues within 4Å: Chain C: G.145, T.146, G.147, A.148, G.149, K.150, S.151, E.167, N.249 Chain D: A.266 Ligands: MG.9 16 PLIP interactions: 2 interactions with chain D, 14 interactions with chain C Water bridges: D:R.290, D:R.290, C:S.151, C:S.151, C:S.151, C:S.152, C:E.167, C:E.167 Hydrogen bonds: C:G.147, C:A.148, C:G.149, C:K.150, C:S.151, C:N.249 Salt bridges: C:K.150, C:K.150 PPV.14: 11 residues within 4Å: Chain A: A.266 Chain D: G.145, T.146, G.147, A.148, G.149, K.150, S.151, E.167, N.249 Ligands: MG.13 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.147, D:A.148, D:G.149, D:K.150, D:S.151, D:N.249 Water bridges: D:S.151, D:S.151, D:S.151, D:S.152, D:E.167, D:E.167, D:R.207 Salt bridges: D:K.150, D:K.150 PPV.18: 11 residues within 4Å: Chain E: G.145, T.146, G.147, A.148, G.149, K.150, S.151, E.167, N.249 Chain F: A.266 Ligands: MG.17 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.147, E:A.148, E:G.149, E:K.150, E:S.151, E:N.249 Water bridges: E:S.151, E:S.151, E:S.151, E:S.152, E:E.167, E:E.167, F:R.290, F:R.290 Salt bridges: E:K.150, E:K.150 PPV.22: 11 residues within 4Å: Chain C: A.266 Chain F: G.145, T.146, G.147, A.148, G.149, K.150, S.151, E.167, N.249 Ligands: MG.21 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.147, F:A.148, F:G.149, F:K.150, F:S.151, F:N.249 Water bridges: F:S.151, F:S.151, F:S.151, F:S.152, F:E.167, F:E.167, F:R.207 Salt bridges: F:K.150, F:K.150

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: D.74, A.77, L.78, A.81, R.196, A.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.74, A:A.197 PEG.4: 6 residues within 4Å: Chain A: A.124, G.125, Y.126, R.196, L.240, G.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.195, A:R.196 Water bridges: A:E.127 PEG.7: 6 residues within 4Å: Chain B: P.86, G.87, F.90, T.160, M.194, Y.199 No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain B: A.81, A.82, S.83 No protein-ligand interaction detected (PLIP) PEG.11: 6 residues within 4Å: Chain C: D.74, A.77, L.78, A.81, R.196, A.197 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.74, C:A.197 PEG.12: 6 residues within 4Å: Chain C: A.124, G.125, Y.126, R.196, L.240, G.241 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.195, C:R.196 Water bridges: C:E.127 PEG.15: 6 residues within 4Å: Chain D: P.86, G.87, F.90, T.160, M.194, Y.199 No protein-ligand interaction detected (PLIP) PEG.16: 3 residues within 4Å: Chain D: A.81, A.82, S.83 No protein-ligand interaction detected (PLIP) PEG.19: 6 residues within 4Å: Chain E: D.74, A.77, L.78, A.81, R.196, A.197 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.74, E:A.197 PEG.20: 6 residues within 4Å: Chain E: A.124, G.125, Y.126, R.196, L.240, G.241 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.195, E:R.196 Water bridges: E:E.127 PEG.23: 6 residues within 4Å: Chain F: P.86, G.87, F.90, T.160, M.194, Y.199 No protein-ligand interaction detected (PLIP) PEG.24: 3 residues within 4Å: Chain F: A.81, A.82, S.83 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY. Int.J.Biol.Macromol. (2022)

Release Date

2022-03-23

Peptides

Packaging NTPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Packaging NTPase

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