SMTL ID : 8ydy.1

Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain B: N.635, T.637 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.635, B:T.637 NAG.2: 4 residues within 4Å: Chain B: N.736, L.941, Q.945, Q.1090 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.736, B:Q.1090 NAG.3: 2 residues within 4Å: Chain B: N.820, S.822 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.820, B:S.822 NAG.4: 2 residues within 4Å: Chain C: N.635, Q.663 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, S. et al., Structure-guided engineering of a mutation-tolerant inhibitor peptide against variable SARS-CoV-2 spikes. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-01-15

Peptides

Spike glycoprotein: ABC
CeSPIACE: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

CeSPIACE

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