SMTL ID : 8ydw.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: D.17, G.22, S.25, L.26 Chain B: Y.121, R.161, S.162, Y.163 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.121, B:Y.121, B:R.161, A:D.17, A:D.17, A:G.22, A:S.25

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain B: N.73, S.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.76 Water bridges: B:N.73, B:S.76, B:S.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, S. et al., Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology. To Be Published

Release Date

2025-01-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SARS-CoV-2 inhibiting peptide CeSPIACE

Spike protein S1

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