SMTL ID : 4qnl.1

Crystal structure of tail fiber protein gp63.1 from E. coli phage G7C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-trimer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: K.692, N.695, D.698, Y.699, P.746, L.747, Y.826 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.692 Water bridges: A:Q.693 PEG.2: 3 residues within 4Å: Chain A: P.198, K.200, D.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.198, A:K.200 PEG.3: 3 residues within 4Å: Chain A: V.532, S.533, W.574 No protein-ligand interaction detected (PLIP) PEG.12: 7 residues within 4Å: Chain B: K.692, N.695, D.698, Y.699, P.746, L.747, Y.826 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.692 Water bridges: B:Q.693 PEG.13: 3 residues within 4Å: Chain B: P.198, K.200, D.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.198, B:K.200 PEG.14: 3 residues within 4Å: Chain B: V.532, S.533, W.574 No protein-ligand interaction detected (PLIP) PEG.23: 7 residues within 4Å: Chain C: K.692, N.695, D.698, Y.699, P.746, L.747, Y.826 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.692 Water bridges: C:Q.693 PEG.24: 3 residues within 4Å: Chain C: P.198, K.200, D.218 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.198, C:K.200 PEG.25: 3 residues within 4Å: Chain C: V.532, S.533, W.574 No protein-ligand interaction detected (PLIP)

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

EDO.4: 3 residues within 4Å: Chain A: N.552, T.554, I.648 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.552 EDO.5: 2 residues within 4Å: Chain A: S.795, S.797 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.795, A:S.797 EDO.15: 3 residues within 4Å: Chain B: N.552, T.554, I.648 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.552 EDO.16: 2 residues within 4Å: Chain B: S.795, S.797 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.795, B:S.797 EDO.26: 3 residues within 4Å: Chain C: N.552, T.554, I.648 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.552 EDO.27: 2 residues within 4Å: Chain C: S.795, S.797 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.795, C:S.797

3 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.25 Chain B: H.25 Chain C: H.25 Ligands: ZN.17, ZN.28 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:H.25, B:H.25, A:H.25 ZN.17: 5 residues within 4Å: Chain A: H.25 Chain B: H.25 Chain C: H.25 Ligands: ZN.6, ZN.28 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:H.25, A:H.25, B:H.25 ZN.28: 5 residues within 4Å: Chain A: H.25 Chain B: H.25 Chain C: H.25 Ligands: ZN.6, ZN.17 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:H.25, A:H.25, B:H.25

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: W.234, A.300, R.359 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.295, A:D.295 Salt bridges: A:R.359 SO4.18: 3 residues within 4Å: Chain B: W.234, A.300, R.359 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.295, B:D.295 Salt bridges: B:R.359 SO4.29: 3 residues within 4Å: Chain C: W.234, A.300, R.359 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.295, C:D.295 Salt bridges: C:R.359

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

CL.8: 2 residues within 4Å: Chain A: N.293, S.294 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: M.247, R.400 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: N.382, D.383, S.384, S.385 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: D.275, S.276, G.345, N.382 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: N.293, S.294 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: M.247, R.400 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: N.382, D.383, S.384, S.385 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: D.275, S.276, G.345, N.382 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain C: N.293, S.294 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain C: M.247, R.400 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain C: N.382, D.383, S.384, S.385 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain C: D.275, S.276, G.345, N.382 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokhorov, N.S. et al., Function of bacteriophage G7C esterase tailspike in host cell adsorption. Mol. Microbiol. (2017)

Release Date

2015-06-24

Peptides

Tail fiber protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Tail fiber protein