SMTL ID : 8ydp.1 (1 other biounit)

Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain B: F.6, G.7, F.10, N.11, V.35, L.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.6, B:F.10, B:L.36 Hydrogen bonds: B:N.11

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain B: G.7, E.8, N.11 No protein-ligand interaction detected (PLIP) GOL.3: 3 residues within 4Å: Chain B: K.126, Q.142, G.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.126, B:Q.142, B:A.143, B:G.144 GOL.4: 1 residues within 4Å: Chain B: F.154 No protein-ligand interaction detected (PLIP)

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 Ce9: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SARS-CoV-2 inhibiting peptide Ce9

Spike protein S1

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