SMTL ID : 7f5h.1 (1 other biounit)

The crystal structure of RBD-Nanobody complex, DL28 (SC4)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 3 residues within 4Å: Chain A: F.12, G.13, N.17 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: N.28, K.30 Chain B: W.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.28, A:N.28 GOL.3: 5 residues within 4Å: Chain B: Y.62, V.66, K.67, G.68, F.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.66, B:G.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., Structural Characterization of a Neutralizing Nanobody With Broad Activity Against SARS-CoV-2 Variants. Front Microbiol (2022)

Release Date

2022-06-29

Peptides

SARS-CoV-2 Spike Receptor-Binding Domain (RBD): A
Nanobody DL28: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

SARS-CoV-2 Spike Receptor-Binding Domain (RBD)

Nanobody DL28

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