SMTL ID : 8zc5.1

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.12, N.39, F.40 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.40 Hydrogen bonds: A:N.12 NAG.2: 2 residues within 4Å: Chain B: N.12, F.40 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep (2024)

Release Date

2024-05-15

Peptides

Spike protein S1: AB
Light chain of D1F6 Fab: CD
Heavy chain of D1F6 Fab: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike protein S1

Light chain of D1F6 Fab

Heavy chain of D1F6 Fab