SMTL ID : 8ydv.2 (1 other biounit)

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Y.10, V.14, D.17, E.18 Chain B: Q.161 Ligands: GOL.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.10, A:D.17, B:Q.161 GOL.2: 10 residues within 4Å: Chain A: M.13, D.17, G.22, S.25, L.26 Chain B: Y.121, Q.161, S.162, Y.163 Ligands: GOL.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.17, A:G.22, A:S.25, B:Q.161, B:S.162 GOL.3: 6 residues within 4Å: Chain B: Y.48, V.75, S.76, I.78, A.79, V.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.48, B:Y.48, B:V.75 GOL.4: 3 residues within 4Å: Chain B: G.72, V.171, Y.176 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain B: W.21, R.23, F.132, R.134 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.23, B:F.132, B:R.134, B:R.134 Water bridges: B:R.134 GOL.6: 4 residues within 4Å: Chain B: G.49, V.50, T.98, F.183 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.50, B:F.183 Water bridges: B:G.49, B:F.183 GOL.7: 4 residues within 4Å: Chain B: F.15, S.17, N.118, Y.119 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:F.15, B:S.17 Water bridges: B:S.17, B:S.17, B:S.17, B:S.17, B:D.110, B:Y.119

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
C

B
D

SARS-CoV-2 inhibiting peptide CeSPIACE

Spike protein S1

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