SMTL ID : 6ean.1

CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT F488I STABILIZED IN THE PREFUSION STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.496, I.499, N.500, L.503 Ligands: NHE.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.499, A:L.503 Hydrogen bonds: A:N.500 NAG.9: 5 residues within 4Å: Chain B: N.496, I.499, N.500, L.503 Ligands: NHE.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.499, B:L.503 Hydrogen bonds: B:N.500 NAG.17: 5 residues within 4Å: Chain C: N.496, I.499, N.500, L.503 Ligands: NHE.19 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.499, C:L.503 Hydrogen bonds: C:N.500

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

NHE.2: 9 residues within 4Å: Chain A: F.137, G.139, F.140, Q.354, I.488 Chain C: F.140 Ligands: SO4.4, NHE.10, NHE.18 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.137, A:I.488, C:F.140, C:F.140 Hydrogen bonds: A:F.137, A:F.140 NHE.3: 9 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.387, A:Y.478 Hydrogen bonds: A:D.479 NHE.10: 9 residues within 4Å: Chain A: F.140 Chain B: F.137, G.139, F.140, Q.354, I.488 Ligands: NHE.2, SO4.12, NHE.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.137, B:I.488, A:F.140, A:F.140 Hydrogen bonds: B:F.137, B:F.140 NHE.11: 9 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.387, B:Y.478 Hydrogen bonds: B:D.479 NHE.18: 9 residues within 4Å: Chain B: F.140 Chain C: F.137, G.139, F.140, Q.354, I.488 Ligands: NHE.2, NHE.10, SO4.20 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.137, C:I.488, B:F.140, B:F.140 Hydrogen bonds: C:F.137, C:F.140 NHE.19: 9 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.387, C:Y.478 Hydrogen bonds: C:D.479

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

SO4.4: 5 residues within 4Å: Chain A: F.137, R.339, Q.354 Chain C: R.106 Ligands: NHE.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:F.137, A:Q.354 Water bridges: A:P.353, C:A.107 Salt bridges: A:R.339, C:R.106 SO4.5: 4 residues within 4Å: Chain A: S.443, K.445, G.464, S.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.443, A:S.466, A:S.466 Salt bridges: A:K.445 SO4.6: 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 SO4.7: 4 residues within 4Å: Chain A: N.444, K.445, G.446, K.461 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.444, A:G.446 Salt bridges: A:K.461 SO4.8: 4 residues within 4Å: Chain A: V.192, L.193, D.194, K.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.192, A:D.194 Salt bridges: A:K.226 SO4.12: 5 residues within 4Å: Chain A: R.106 Chain B: F.137, R.339, Q.354 Ligands: NHE.10 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:R.106, A:A.107 Salt bridges: A:R.106, B:R.339 Hydrogen bonds: B:F.137, B:Q.354 SO4.13: 4 residues within 4Å: Chain B: S.443, K.445, G.464, S.466 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.443, B:S.466, B:S.466 Salt bridges: B:K.445 SO4.14: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.276, B:N.277 Salt bridges: B:R.364 SO4.15: 4 residues within 4Å: Chain B: N.444, K.445, G.446, K.461 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.444, B:G.446 Salt bridges: B:K.461 SO4.16: 4 residues within 4Å: Chain B: V.192, L.193, D.194, K.226 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.192, B:D.194 Salt bridges: B:K.226 SO4.20: 5 residues within 4Å: Chain B: R.106 Chain C: F.137, R.339, Q.354 Ligands: NHE.18 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:F.137, C:Q.354 Salt bridges: C:R.339, B:R.106 Water bridges: B:R.106, B:A.107 SO4.21: 4 residues within 4Å: Chain C: S.443, K.445, G.464, S.466 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.443, C:S.466, C:S.466 Salt bridges: C:K.445 SO4.22: 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 SO4.23: 4 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.444, C:G.446 Salt bridges: C:K.461 SO4.24: 4 residues within 4Å: Chain C: V.192, L.193, D.194, K.226 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.192, C:D.194 Salt bridges: C:K.226

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
F

B
F

C
F

Fusion glycoprotein F0