SMTL ID : 9fc2.1

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: G.10, F.13, N.14, L.39 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.9

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: D.99, F.100, T.101, F.135, S.185, F.186, E.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.99, A:T.101 Water bridges: A:D.99, A:T.101 EDO.4: 6 residues within 4Å: Chain B: S.7, G.8, R.19, L.20, S.21, Y.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.7, B:S.21

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 8 residues within 4Å: Chain B: C.22, A.24, T.31, L.34, Q.70, N.75, T.76, I.98 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.24, B:L.34 Hydrogen bonds: B:N.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerdan, L. et al., Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants. Mabs (2025)

Release Date

2025-06-11

Peptides

Spike protein S1: A
Nanobody 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike protein S1

Nanobody 4