SMTL ID : 8j1v.1

Cryo-EM structure of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: Y.4, N.6, N.37 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.254, E.255, N.256 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.1048 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.96, N.99 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: S.86, Q.89, N.139 Chain G: R.331 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.208 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.305, Q.554 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain D: Y.4, N.6, N.37 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain D: N.254, E.255, N.256 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain D: N.577 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain D: N.631 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain D: N.1048 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: N.96, N.99 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: R.331 Chain D: S.86, Q.89, N.139 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain D: N.208 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: N.305, Q.554 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain G: Y.4, N.6, N.37 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain G: N.254, E.255, N.256 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain G: N.577 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain G: N.631 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain G: N.1048 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain G: N.96, N.99 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: R.331 Chain G: S.86, Q.89, N.139 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain G: N.208 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain G: N.305, Q.554 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tai, W. et al., A lung-selective delivery of mRNA encoding broadly neutralizing antibody against SARS-CoV-2 infection. Nat Commun (2023)

Release Date

2023-11-29

Peptides

Spike protein S2': ADG
8-9D heavy chain: BEH
8-9D light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
K

F
D

I
G

Spike protein S2'

8-9D heavy chain

8-9D light chain

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