SMTL ID : 6eai.1

CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT S398L STABILIZED IN THE PREFUSION STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.496, N.500 Ligands: NHE.6 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: N.500 Ligands: SO4.11, NHE.13 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain C: N.496, N.500 Ligands: NHE.21 No protein-ligand interaction detected (PLIP)

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

SO4.2: 4 residues within 4Å: Chain A: F.137, R.339, Q.354 Ligands: NHE.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.137, A:Q.354 Salt bridges: A:R.339 SO4.3: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.443, A:S.443, A:S.466, A:S.466 SO4.4: 4 residues within 4Å: Chain A: L.273, N.276, N.277, R.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.276, A:N.277 Salt bridges: A:R.364 SO4.8: 5 residues within 4Å: Chain B: F.137, R.339, Q.354, E.356 Ligands: NHE.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.137, B:Q.354, B:Q.354 Salt bridges: B:R.339 SO4.9: 5 residues within 4Å: Chain B: S.443, K.445, G.464, K.465, S.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.443, B:S.443, B:S.466 SO4.10: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.277 Salt bridges: B:R.364 SO4.11: 2 residues within 4Å: Ligands: NAG.7, NHE.13 No protein-ligand interaction detected (PLIP) SO4.16: 5 residues within 4Å: Chain C: F.137, R.339, Q.354, E.356 Ligands: NHE.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.137, C:Q.354, C:Q.354 Salt bridges: C:R.339 SO4.17: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.443, C:G.464, C:S.466 SO4.18: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.276, C:N.277 Salt bridges: C:R.364 SO4.19: 2 residues within 4Å: Chain C: I.148, V.243 No protein-ligand interaction detected (PLIP)

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

NHE.5: 9 residues within 4Å: Chain A: F.137, G.139, F.140, Q.354, F.488 Chain C: F.140 Ligands: SO4.2, NHE.12, NHE.20 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:F.140, A:F.137, A:F.137, A:F.488 Hydrogen bonds: A:G.139, A:F.140, A:Q.354 NHE.6: 8 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, V.482, N.496, I.499 Ligands: NAG.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.387, A:F.387, A:F.477 Hydrogen bonds: A:F.477, A:D.479, A:N.496 NHE.12: 9 residues within 4Å: Chain A: F.140 Chain B: F.137, G.139, F.140, Q.354, F.488 Ligands: NHE.5, SO4.8, NHE.20 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.137, B:F.488, A:F.140 Hydrogen bonds: B:F.137, B:G.139, B:F.140 NHE.13: 10 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.7, SO4.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477 Hydrogen bonds: B:D.479, B:N.496 NHE.20: 8 residues within 4Å: Chain C: F.137, G.139, F.140, Q.354, F.488 Ligands: NHE.5, NHE.12, SO4.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.137, C:F.137, C:F.488, C:F.488 NHE.21: 9 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477 Hydrogen bonds: C:D.479, C:N.496

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

TAR.14: 2 residues within 4Å: Chain B: S.186, P.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.186, B:S.186 TAR.22: 6 residues within 4Å: Chain C: N.426, K.427, N.428, R.429, G.446, D.448 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.426, C:R.429, C:R.429, C:G.446, C:D.448 Salt bridges: C:K.427, C:R.429, C:R.429, C:K.461

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance. To be published

Release Date

2019-08-07

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fusion glycoprotein F0