SMTL ID : 7x2l.1

Crystal structure of nanobody 3-2A2-4 with SARS-CoV-2 RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 10 residues within 4Å: Chain A: N.11, S.39, S.41, F.42, W.104 Chain B: Q.1, F.103, Y.104, Y.105, W.106 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.42, A:W.104, B:Q.1 Hydrogen bonds: A:S.41, B:Q.1, B:Y.105 Water bridges: A:N.105, A:S.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses. Nat Commun (2022)

Release Date

2022-12-07

Peptides

Spike protein S1: A
Nanobody 3-2A2-4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
B

Spike protein S1

Nanobody 3-2A2-4

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