SMTL ID : 8yds.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 5 residues within 4Å: Chain B: F.6, G.7, F.10, N.11, L.36 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain B: F.10, N.11, A.40, W.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.11 Water bridges: B:S.41 GOL.3: 8 residues within 4Å: Chain B: T.44, K.46, Y.48, V.75, R.76, I.78, A.79, V.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.46, B:Y.48 Water bridges: B:T.44, B:R.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 Ce59: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SARS-CoV-2 inhibiting peptide Ce59

Spike protein S1

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