SMTL ID : 8ydz.1

Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 2 residues within 4Å: Chain A: N.350, Q.599 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.635, T.637 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.736, L.941, Q.945, Q.1090 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.820, S.822 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain B: P.349, N.350, Q.599 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain B: N.622 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain B: N.635, T.637 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.728, G.1150 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: N.736, L.941, Q.945, Q.1090 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.820, S.822 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: N.1117, T.1119, H.1120, F.1122 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain C: N.350, Q.599, L.601 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.622 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.635, Q.663 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: D.815 Chain C: N.728, I.1149 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: N.736, L.941, Q.945, Q.1090 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: N.820, S.822 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: N.1117, T.1119, H.1120, F.1122 Ligand excluded by 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

Spike glycoprotein: ABC
CeSPIACE: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
H

Spike glycoprotein

CeSPIACE

Related Entries With Identical Sequence