SMTL ID : 8q7s.1 (4 other biounits)

Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.1: 10 residues within 4Å: Chain A: S.29, N.30, C.31, V.32, A.33, N.58, L.60, C.61, F.62, T.63 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.32 Hydrogen bonds: A:F.62

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

EDO.2: 6 residues within 4Å: Chain A: N.107, V.173, Q.176 Chain B: E.48, W.49 Ligands: EDO.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.107, A:N.107, A:Q.176, B:W.49 EDO.3: 3 residues within 4Å: Chain A: N.107 Chain B: W.49 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.107 Water bridges: A:S.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aksu, M. et al., Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters. Antiviral Res. (2023)

Release Date

2023-12-20

Peptides

Spike protein S1: A
VHH Antibody Re21H01: B
VHH Antibody Ma6F06: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1

VHH Antibody Re21H01

VHH Antibody Ma6F06

Related Entries With Identical Sequence