SMTL ID : 7whk.1

The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-3-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: E.130, N.159, N.160 Chain E: Y.30, D.31 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: E.278, N.279 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: Y.704, S.705, N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: T.713, N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain B: N.120, A.121, T.122, N.123, V.125, F.152 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.277, E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: Y.793 Chain B: S.705, N.706 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.798, Q.801 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: V.118, N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain C: Q.113, E.130, N.159, N.160, C.161, T.162 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: I.791, Y.793 Chain C: Y.704, S.705, N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody. Cell (2022)

Release Date

2022-05-11

Peptides

Spike glycoprotein: ABC
Bn03_nano2: DH
Bn03_nano1: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

H
H

E
E

F
F

G
G

Spike glycoprotein

Bn03_nano2

Bn03_nano1

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