SMTL ID : 7mfu.1 (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

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

EDO.1: 4 residues within 4Å: Chain A: F.11, N.12, S.42, W.105 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.42 EDO.2: 8 residues within 4Å: Chain A: T.169, N.170, G.171 Chain B: T.56, T.58, A.59, Y.60, K.65 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.171, B:K.65 EDO.4: 4 residues within 4Å: Chain C: T.55, G.58, L.74, N.76 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.55, C:N.76 Water bridges: C:L.74, C:L.74

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain C: A.26, I.30, L.36, T.55, L.74, N.76, N.79, T.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.79 Water bridges: C:I.33

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
A

B
B

C
C

Spike protein S1

Synthetic Nanobody #14 (Sb14)

Synthetic nanobody #68 (Sb68)

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