SMTL ID : 5ea8.1

Crystal Structure of Prefusion RSV F Glycoprotein Fusion Inhibitor Resistance Mutant D489Y

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: F.137, R.339 Chain C: R.106, A.107, F.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.137, A:F.137 Salt bridges: A:R.339 SO4.2: 3 residues within 4Å: Chain A: N.426, N.428, R.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.426 Salt bridges: A:R.429 SO4.3: 5 residues within 4Å: Chain A: F.137, L.138, G.139, F.140, Q.354 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.137, A:G.139, A:F.140, A:Q.354 Water bridges: A:F.137 SO4.4: 4 residues within 4Å: Chain A: S.443, K.445, G.464, S.466 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.443, A:S.466, A:S.466 SO4.5: 2 residues within 4Å: Chain A: K.293, E.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.294 SO4.8: 5 residues within 4Å: Chain A: R.106, A.107, F.140 Chain B: F.137, R.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.137, B:F.137 Salt bridges: B:R.339 SO4.9: 3 residues within 4Å: Chain B: N.426, N.428, R.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.426 Salt bridges: B:R.429 SO4.10: 5 residues within 4Å: Chain B: F.137, L.138, G.139, F.140, Q.354 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.137, B:G.139, B:F.140, B:Q.354 Water bridges: B:F.137 SO4.11: 4 residues within 4Å: Chain B: S.443, K.445, G.464, S.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.443, B:S.466, B:S.466 SO4.12: 2 residues within 4Å: Chain B: K.293, E.294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.294 SO4.15: 5 residues within 4Å: Chain B: R.106, A.107, F.140 Chain C: F.137, R.339 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.137, C:F.137 Salt bridges: C:R.339 SO4.16: 3 residues within 4Å: Chain C: N.426, N.428, R.429 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.426 Salt bridges: C:R.429 SO4.17: 5 residues within 4Å: Chain C: F.137, L.138, G.139, F.140, Q.354 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.137, C:G.139, C:F.140, C:Q.354 SO4.18: 4 residues within 4Å: Chain C: S.443, K.445, G.464, S.466 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.443, C:S.466, C:S.466 SO4.19: 2 residues within 4Å: Chain C: K.293, E.294 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.294

3 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.6: 7 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.387, A:F.477, A:Y.478 Hydrogen bonds: A:D.479 NHE.13: 7 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477, B:Y.478 Hydrogen bonds: B:D.479 NHE.20: 7 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477, C:Y.478 Hydrogen bonds: C:D.479

3 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.7: 3 residues within 4Å: Chain A: T.174, N.175, K.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.174, A:N.175, A:N.175 TAR.14: 3 residues within 4Å: Chain B: T.174, N.175, K.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.175, B:N.175 TAR.21: 3 residues within 4Å: Chain C: T.174, N.175, K.176 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.174, C:N.175, C:N.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Molecular mechanism of respiratory syncytial virus fusion inhibitors. Nat.Chem.Biol. (2016)

Release Date

2015-12-09

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0