SMTL ID : 8ydx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain D: E.300, N.301 Chain F: N.575, K.577 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain D: N.350, Q.599, L.601 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain D: N.635, Q.663 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain D: N.728, I.1149 Chain E: D.815 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain D: N.736, L.941, Q.945, Q.1090 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain D: N.1117, T.1119, H.1120, F.1122 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain D: S.730, N.1093, F.1094, T.1095 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain D: N.1153 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain D: N.820, S.822, Q.823 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain E: N.299, E.300, N.301 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain E: P.349, N.350, I.351, Q.599 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain E: N.635, T.637 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain E: N.728, G.1150 Chain F: D.815 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain E: N.736, L.941, Q.945, Q.1090 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain E: N.820, S.822 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain E: A.725, E.1091, K.1092, N.1093 Chain F: Q.914 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain E: N.1117, T.1119, H.1120, F.1122 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain E: N.1153 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain F: E.300, N.301 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain F: N.350, Q.599 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain F: N.635 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain F: N.728, G.1150 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain F: N.736, L.941, Q.945, Q.1090 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain F: N.820, S.822 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: Q.914 Chain F: A.725, N.1093 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain F: N.1117, T.1119, H.1120, F.1122 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain F: N.1153 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

CeSPIACE: ABC
Spike glycoprotein: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

C
E

D
C

E
B

F
A

CeSPIACE

Spike glycoprotein

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