SMTL ID : 8vq9.1

Prefusion stabilized structure of the SARS-CoV-2 fusion machinery

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.64, L.269, Q.273 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.269 NAG-NAG.2: 3 residues within 4Å: Chain A: N.148, S.150, Q.151 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.445, H.448, F.450 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.64, L.269, Q.273 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.269 NAG-NAG.5: 3 residues within 4Å: Chain B: N.148, S.150, Q.151 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.445, H.448, F.450 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.64, L.269, Q.273 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.269 NAG-NAG.8: 3 residues within 4Å: Chain C: N.148, S.150, Q.151 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.445, H.448, F.450 No protein-ligand interaction detected (PLIP)

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

NAG.10: 1 residues within 4Å: Chain A: N.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.56 NAG.11: 4 residues within 4Å: Chain A: E.419, K.420, N.421 Chain C: Q.242 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.421, C:Q.242 NAG.12: 1 residues within 4Å: Chain A: N.481 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain B: N.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.56 NAG.14: 4 residues within 4Å: Chain A: Q.242 Chain B: E.419, K.420, N.421 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.421, A:Q.242 NAG.15: 1 residues within 4Å: Chain B: N.481 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain C: N.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.56 NAG.17: 4 residues within 4Å: Chain B: Q.242 Chain C: E.419, K.420, N.421 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.242, C:N.421 NAG.18: 1 residues within 4Å: Chain C: N.481 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J. et al., A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines. Nat Commun (2024)

Release Date

2024-07-24

Peptides

Spike protein S2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S2