SMTL ID : 7ns6.1

SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain G: N.331, P.579, Q.580, T.581 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.331 NAG-NAG-BMA.2: 2 residues within 4Å: Chain H: G.339, N.343 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain G: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain G: S.708, N.709, N.710 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain G: N.1134 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain G: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain G: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain G: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain G: N.1098, T.1100 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain H: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain H: I.1132, N.1134 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain H: N.709, N.710, P.1079, I.1130, G.1131 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain H: N.331, Q.580 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain H: N.801, S.803 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain H: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain H: N.616 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain I: N.1134 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain G: D.796 Chain I: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain I: N.801, S.803 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain I: N.717, F.718, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain I: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain I: N.331 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain I: G.339, F.342, N.343, F.374 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain H: K.558 Chain I: E.281, N.282 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain I: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain I: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain J: N.801, S.803 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain J: F.338, G.339, F.342, N.343, S.371 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain J: N.1098, G.1099, F.1103 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain J: N.1134 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain J: N.331, I.332, Q.580, L.582 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain J: N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain J: S.708, N.709 Chain K: D.796 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain J: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain K: N.709, G.1131 Chain L: D.796 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain K: N.1098, G.1099, T.1100, F.1103 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain K: N.1134 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain K: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain K: G.799, N.801, N.928 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain L: N.801, S.803 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain L: T.716, N.717, L.922, F.1109 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain L: N.1134 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain L: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain L: R.328, F.329, P.330, N.331, S.530 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain L: F.338, G.339, F.342, N.343, F.374 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain L: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain L: N.1098, H.1101, F.1103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanke, L. et al., A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun (2022)

Release Date

2022-02-02

Peptides

Fu2 nanobody: ABCDEF
Spike glycoprotein,Fibritin: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
S

C
H

D
T

E
O

F
U

G
I

H
K

I
M

J
J

K
L

L
N

Fu2 nanobody

Spike glycoprotein,Fibritin

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