SMTL ID : 7b18.1

SARS-CoV-spike bound to two neutralising nanobodies

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain C: G.339, N.343, S.371 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: N.331, I.332, T.333, Q.580 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: F.338, F.342, L.368 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.717, L.922 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: Q.14, C.15, N.17, N.137 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.122, T.124, N.125 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: F.342, N.343, F.374 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: S.711, N.1074, F.1075, T.1076 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: I.233, N.234 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koenig, P.A. et al., Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. Science (2021)

Release Date

2021-04-28

Peptides

Spike glycoprotein: ABC
Nanobody against SARS-CoV-2 VHH E: DFH
Nanobody against spike glycoprotein VHH V: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

Spike glycoprotein

Nanobody against SARS-CoV-2 VHH E

Nanobody against spike glycoprotein VHH V

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