SMTL ID : 8z64.1

Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation (focused refinement of NTD-SD1-RBD-ACE2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

6 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, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.122, T.124, V.127, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.5: 1 residues within 4Å: Chain C: N.90 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: S.420, N.546 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain B: N.280, E.281, N.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.280, B:E.281, B:N.282 NAG.8: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: N.148, N.149, M.153 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.148 Hydrogen bonds: B:N.148 NAG.10: 3 residues within 4Å: Chain B: Q.115, E.132, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.132 NAG.11: 1 residues within 4Å: Chain B: N.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.234 NAG.12: 5 residues within 4Å: Chain C: Q.81, N.103, V.107, N.194, H.195 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.81, C:Q.81 NAG.13: 1 residues within 4Å: Chain C: N.322 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.322, C:N.322 NAG.14: 2 residues within 4Å: Chain C: N.432, W.594 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.432 NAG.15: 3 residues within 4Å: Chain C: N.53, T.55, Q.340 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.340

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: AB
Angiotensin-converting enzyme 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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