SMTL ID : 8z7b.1

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-mer

Ligands

7 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: 1 residues within 4Å: Chain A: N.90 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 NAG-NAG.4: 5 residues within 4Å: Chain B: N.122, T.124, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.5: 6 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, W.152, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.28 NAG-NAG.7: 6 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, V.367, L.368 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.8: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP)

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

NAG.9: 2 residues within 4Å: Chain A: N.53, Q.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53 NAG.10: 5 residues within 4Å: Chain A: Q.81, Q.101, N.103, V.107, H.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.81 NAG.11: 1 residues within 4Å: Chain A: N.322 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.432, W.594 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain B: Q.115, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.115 NAG.15: 2 residues within 4Å: Chain B: N.282 Chain C: K.558 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.282, C:K.558, C:K.558

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

Angiotensin-converting enzyme 2: A
Spike glycoprotein: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
A

Angiotensin-converting enzyme 2

Spike glycoprotein

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