SMTL ID : 9co6.1

BA.5 spike/Nanosota-9 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

8 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: 4 residues within 4Å: Chain A: N.1103, T.1105, H.1106, F.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.722, L.927, Q.931 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.806, S.808, Q.809 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.1139 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.722, L.927, Q.931, Q.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.806, S.808, Q.809 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.1103, T.1105, H.1106, F.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.1139 No protein-ligand interaction detected (PLIP)

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

NAG.9: 2 residues within 4Å: Chain A: Y.35, N.68 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.285, E.286, N.287 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.806, S.808, Q.809 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.722, Q.931 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.714 Chain C: Y.801 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.336, Q.585 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.621, T.623, Q.649 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: N.285, E.286, N.287 Chain C: K.563 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.621, Q.649 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: Y.660, N.662 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1079 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: I.799, Y.801 Chain B: N.714 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1103, T.1105, H.1106, F.1108 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.336, P.584, Q.585 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: Y.35, T.36, N.37, N.68 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: E.286, N.287, T.289 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.621, T.623, Q.649 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: I.799 Chain C: N.714 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.1079 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.336, Q.585, L.587 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate. Plos Pathog. (2024)

Release Date

2024-11-20

Peptides

Spike glycoprotein: ABC
Nanosota-9: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
E

E
F

F
D

Spike glycoprotein

Nanosota-9

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