SMTL ID : 8jva.1

Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N235 and S2L20 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain D: N.120, T.122 No protein-ligand interaction detected (PLIP) NAG.2: 1 residues within 4Å: Chain D: N.160 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: Q.1, G.26 Chain D: E.278, N.279 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.277, D:E.278, D:E.278, A:G.26 NAG.4: 3 residues within 4Å: Chain B: R.51 Chain C: R.124 Chain D: N.231 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.51, C:R.124 NAG.5: 3 residues within 4Å: Chain C: S.96 Chain D: F.59, N.61 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., Enhanced potency of an IgM-like nanobody targeting conserved epitope in SARS-CoV-2 spike N-terminal domain. Signal Transduct Target Ther (2024)

Release Date

2024-05-22

Peptides

nanobody N235: A
S2L20 light chain: B
S2L20 heavy chain: C
Spike protein S2': D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
F

nanobody N235

S2L20 light chain

S2L20 heavy chain

Spike protein S2'