SMTL ID : 7fh0.1

Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-2-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: F.20, G.21, N.25, S.53 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: F.239, G.240, N.244, S.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.272

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: R.85, K.99, Y.187 Chain B: W.50, S.51, D.52 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.85, A:K.99, A:Y.187, B:S.51 PEG.4: 3 residues within 4Å: Chain A: K.140, I.369 Chain B: H.103 No protein-ligand interaction detected (PLIP) PEG.5: 5 residues within 4Å: Chain A: Y.171 Chain B: D.52, T.53, W.97, R.100 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.171 Hydrogen bonds: B:D.52

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: V.384 Chain B: Y.193, G.199, F.201, T.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.199, B:G.199 GOL.7: 8 residues within 4Å: Chain A: V.165 Chain C: Y.193, V.197, K.198, G.199, R.200, F.201, T.202 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.193, C:V.197, C:K.198, C:K.198, C:G.199, C:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, H. et al., Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron. Cell Res. (2022)

Release Date

2022-08-03

Peptides

Spike protein S1,Spike protein S1: A
nanobodies aRBD-2-7: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1,Spike protein S1

nanobodies aRBD-2-7