SMTL ID : 7mfu.2 (1 other biounit)

Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: K.47, Y.49, V.76, R.77, I.79, A.80, V.102 Chain C: D.113 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.47, A:Y.49, C:D.113 EDO.2: 7 residues within 4Å: Chain A: N.170, G.171 Chain B: T.56, T.58, A.59, Y.60, K.65 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.171, B:Y.60 Water bridges: B:K.65 EDO.3: 4 residues within 4Å: Chain A: Y.158 Chain B: Q.39, R.45, Y.95 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.45, B:R.45 Water bridges: B:Q.39, B:Y.95, B:Y.95, A:G.154 EDO.4: 5 residues within 4Å: Chain C: A.26, I.33, L.74, N.76, N.79 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.76, C:N.79, C:N.79 EDO.5: 6 residues within 4Å: Chain C: Q.111, D.112, D.113, Y.114, W.115, W.117 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, J. et al., Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem. (2021)

Release Date

2021-06-02

Peptides

Spike protein S1: A
Synthetic Nanobody #14 (Sb14): B
Synthetic nanobody #68 (Sb68): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Spike protein S1

Synthetic Nanobody #14 (Sb14)

Synthetic nanobody #68 (Sb68)

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