SMTL ID : 8z7l.1

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of S-bottom)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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.331, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.616, T.618 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.616 NAG.5: 3 residues within 4Å: Chain A: N.280, E.281, N.282 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.281 Hydrogen bonds: A:E.281 NAG.6: 2 residues within 4Å: Chain B: N.616, T.618 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.616 NAG.7: 3 residues within 4Å: Chain B: N.280, E.281, N.282 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.281 Hydrogen bonds: B:E.281 NAG.8: 2 residues within 4Å: Chain C: N.616, T.618 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.616 NAG.9: 3 residues within 4Å: Chain C: N.280, E.281, N.282 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.281 Hydrogen bonds: C:E.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xing, L. et al., Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target. Cell (2025)

Release Date

2025-02-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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