SMTL ID : 7whj.1

The state 1 complex structure of Omicron spike with Bn03 (1-up RBD, 3 nanobodies)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.2: 5 residues within 4Å: Chain A: K.111, E.130, N.159, N.160 Chain D: D.31 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.231 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.277, N.279 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.340 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: A.703, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.120, A.121, N.123, V.125 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: E.462 Chain B: T.106, N.231 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: F.335, N.340, N.367 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1071 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.160 Chain F: G.66 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.231 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: K.555 Chain C: N.277, N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.340 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: Y.793 Chain C: S.705, N.706 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: Q.892 Chain C: A.703, N.1071 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.613 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_nano1: DE
Bn03_nano2: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Bn03_nano1

Bn03_nano2

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