SMTL ID : 6eal.1

CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT D486N STABILIZED IN THE PREFUSION STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

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

TAR.1: 6 residues within 4Å: Chain A: F.137 Chain C: F.140, F.488 Ligands: TAR.2, TAR.7, TAR.13 No protein-ligand interaction detected (PLIP) TAR.2: 8 residues within 4Å: Chain A: F.137, L.138, G.139, F.140, P.353, Q.354, E.356 Ligands: TAR.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.137, A:F.137, A:F.137, A:G.139, A:F.140, A:Q.354 TAR.3: 4 residues within 4Å: Chain A: Y.53, S.186, D.263, P.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.186 TAR.7: 6 residues within 4Å: Chain A: F.140, F.488 Chain B: F.137 Ligands: TAR.1, TAR.8, TAR.13 No protein-ligand interaction detected (PLIP) TAR.8: 8 residues within 4Å: Chain B: F.137, L.138, G.139, F.140, P.353, Q.354, E.356 Ligands: TAR.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.137, B:F.137, B:F.137, B:G.139, B:F.140, B:Q.354 TAR.9: 4 residues within 4Å: Chain B: Y.53, S.186, D.263, P.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.53, B:S.186 TAR.13: 6 residues within 4Å: Chain B: F.140, F.488 Chain C: F.137 Ligands: TAR.1, TAR.7, TAR.14 No protein-ligand interaction detected (PLIP) TAR.14: 8 residues within 4Å: Chain C: F.137, L.138, G.139, F.140, P.353, Q.354, E.356 Ligands: TAR.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.137, C:F.137, C:G.139, C:F.140, C:Q.354 TAR.15: 4 residues within 4Å: Chain C: Y.53, S.186, D.263, P.265 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.186

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

SO4.4: 3 residues within 4Å: Chain A: K.419, K.421 Chain C: A.346 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.419, A:K.421 Water bridges: C:S.348, C:S.348 SO4.5: 4 residues within 4Å: Chain A: Q.283, Q.284, T.357, K.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.284, A:K.359 SO4.10: 3 residues within 4Å: Chain A: A.346 Chain B: K.419, K.421 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.419, B:K.421 Water bridges: A:S.348, A:S.348 SO4.11: 4 residues within 4Å: Chain B: Q.283, Q.284, T.357, K.359 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.284, B:K.359 SO4.16: 3 residues within 4Å: Chain B: A.346 Chain C: K.419, K.421 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.419, C:K.421 Water bridges: B:S.348, B:S.348 SO4.17: 4 residues within 4Å: Chain C: Q.283, Q.284, T.357, K.359 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.284, C:K.359

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

NHE.6: 6 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, N.496, I.499 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.479, A:I.499, A:I.499 NHE.12: 6 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, N.496, I.499 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.479, B:I.499, B:I.499 NHE.18: 6 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, N.496, I.499 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.479, C:I.499, C:I.499

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