SMTL ID : 9co8.1

JN.1 spike/Nanosota-9 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

16 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: 2 residues within 4Å: Chain A: N.622, T.624 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.715 Chain C: I.800, Y.802 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.723, L.928, Q.932 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.928 NAG-NAG.4: 3 residues within 4Å: Chain A: N.807, S.809, Q.810 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1104, T.1106, H.1107, F.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1140 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: Y.802 Chain B: N.715 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.723, L.928, Q.932, Q.1077 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.928 NAG-NAG.9: 3 residues within 4Å: Chain B: N.807, S.809, Q.810 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.1104, T.1106, H.1107, F.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1140 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: I.800, Y.802 Chain C: N.715 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.723, L.928, Q.932, Q.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.807, S.809, Q.810 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.1104, T.1106, H.1107, F.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1140 No protein-ligand interaction detected (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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