SMTL ID : 9iqp.1

Crystal structure of the Wuhan SARS-CoV-2 Spike RBD (319-541) complexed with 1p1B10 nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: F.20, G.21, F.24, N.25, L.50 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.20, A:F.24, A:L.50 Water bridges: A:N.25

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain B: V.29, H.30, S.32, D.33, M.34, Q.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.32, B:Q.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shcheblyakov, D.V. et al., Ultra-potent RBM-specific single-domain antibody broadly neutralizes multiple SARS-CoV-2 variants with picomolar activity. Int.J.Biol.Macromol. (2025)

Release Date

2025-07-16

Peptides

Spike protein S1: A
Nanobody 1p1B10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike protein S1

Nanobody 1p1B10

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