SMTL ID : 6orj.1

Central spike of phiKZ phage tail

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-trimer

Ligands

15 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: W.88, P.90, N.91, R.95, P.99 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: K.222, D.229 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: Q.117 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.37, F.38, T.39 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: G.147, N.151, F.152, D.153, T.154, C.155 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: W.88, P.90, N.91, R.95, P.99 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.222, D.229 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: Q.117 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: S.37, F.38, T.39 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: G.147, N.151, F.152, D.153, T.154, C.155 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain C: W.88, P.90, N.91, R.95, P.99 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: K.222, D.229 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain C: Q.117 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: S.37, F.38, T.39 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain C: G.147, N.151, F.152, D.153, T.154, C.155 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: F.21, Q.117, Y.119 Chain B: L.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.117, A:Y.119, A:Y.119 EDO.15: 4 residues within 4Å: Chain B: F.21, Q.117, Y.119 Chain C: L.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.117, B:Y.119, B:Y.119 EDO.24: 4 residues within 4Å: Chain A: L.125 Chain C: F.21, Q.117, Y.119 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.117, C:Y.119, C:Y.119

9 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: N.91 Chain B: N.91 Chain C: N.91 Ligands: NA.16, NA.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.91 NA.8: 2 residues within 4Å: Chain A: Y.235 Chain B: D.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.229 NA.9: 2 residues within 4Å: Chain A: D.100, S.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100, A:S.134 NA.16: 5 residues within 4Å: Chain A: N.91 Chain B: N.91 Chain C: N.91 Ligands: NA.7, NA.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.91 NA.17: 2 residues within 4Å: Chain B: Y.235 Chain C: D.229 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.229 NA.18: 2 residues within 4Å: Chain B: D.100, S.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.134, B:S.134 NA.25: 5 residues within 4Å: Chain A: N.91 Chain B: N.91 Chain C: N.91 Ligands: NA.7, NA.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.91 NA.26: 2 residues within 4Å: Chain A: D.229 Chain C: Y.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.229 NA.27: 2 residues within 4Å: Chain C: D.100, S.134 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.134, C:S.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leiman, P.G. et al., Central spike of phiKZ phage tail. To Be Published

Release Date

2019-06-19

Peptides

PHIKZ164: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

PHIKZ164