SMTL ID : 8dm4.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.119, T.121, N.122, V.124, E.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.122

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

NAG.2: 2 residues within 4Å: Chain A: Y.25, N.58 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: E.129, N.162 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: T.105, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep (2023)

Release Date

2023-01-25

Peptides

Spike glycoprotein: A
Fab 4A8 heavy chain: B
Fab 4A8 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

Fab 4A8 heavy chain

Fab 4A8 light chain

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