SMTL ID : 7xrp.1

Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2 (localized refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: S.86, E.106, N.139 Chain B: F.28, R.104 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.86, B:R.104 NAG.2: 3 residues within 4Å: Chain A: N.254, E.255, N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.254 NAG.3: 3 residues within 4Å: Chain A: N.96, A.97, V.101 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain C: G.10, F.13, N.14, V.38 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.13 Hydrogen bonds: C:V.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, D. et al., A potent synthetic nanobody with broad-spectrum activity neutralizes SARS-CoV-2 virus and the Omicron variant BA.1 through a unique binding mode. J Nanobiotechnology (2022)

Release Date

2022-10-05

Peptides

Spike protein S1: A
C5G2 nanobody: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

Spike protein S1

C5G2 nanobody

Spike protein S1