SMTL ID : 9fr3.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with nanobody 7F

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain B: N.109, T.111, V.114 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain B: N.221, T.223 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain B: N.267, E.268, N.269 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain D: Y.15, N.48 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain D: N.109, T.111, V.114 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain D: N.152 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain D: N.221, T.223 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain D: N.267, E.268, N.269 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.696, G.1118 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain F: Y.15, N.48 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain F: N.109, T.111, V.114 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain F: N.152 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain F: N.221, T.223 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain F: N.267, E.268, N.269 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain F: N.696, G.1118 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain H: Y.15, N.48 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain H: N.109, T.111, V.114 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain H: N.152 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain H: N.221, T.223 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain H: N.267, E.268, N.269 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain H: N.603 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain H: N.696, G.1118 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain J: Y.15, N.48 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain J: N.109, T.111, V.114 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain J: N.152 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain J: N.221, T.223 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain J: N.267, E.268, N.269 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain J: N.603 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain J: N.696, G.1118 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain L: Y.15, N.48 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain L: N.109, T.111, V.114 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain L: N.152 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain L: N.221, T.223 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain L: N.267, E.268, N.269 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain L: N.603 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain L: N.696, G.1118 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debski-Antoniak, O. et al., A Spike Trimer Dimer-Inducing Nanobody with Anti-Sarbecovirus Activity. To Be Published

Release Date

2025-03-19

Peptides

Nanobody 7F: ACEGIK
Spike glycoprotein: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
E

E
F

G
I

I
K

K
L

B
A

D
B

F
D

H
G

J
H

L
J

Nanobody 7F

Spike glycoprotein

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