SMTL ID : 8ydq.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with Ce149

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: M.13, D.17, G.22, S.25, L.26 Chain B: Y.121, R.161, S.162, Y.163 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.121, B:Y.121, B:R.161, A:D.17, A:G.22, A:S.25

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

SARS-CoV-2 inhibiting peptide Ce149: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SARS-CoV-2 inhibiting peptide Ce149

Spike protein S1

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