SMTL ID : 9ato.1

XBB.1.5 spike/Nanosota-3C complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.700, L.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: A.689, E.1055, N.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.700, L.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: A.689, E.1055, N.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.700, L.905, Q.909, Q.1054 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.905 NAG-NAG.12: 3 residues within 4Å: Chain C: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1117 No protein-ligand interaction detected (PLIP)

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.16: 1 residues within 4Å: Chain A: N.265 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain A: N.314, Q.563 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.314 NAG.18: 3 residues within 4Å: Chain A: N.692 Chain B: I.777, Y.779 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain B: N.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.45 NAG.20: 3 residues within 4Å: Chain B: N.314, P.562, Q.563 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.314, B:P.562 NAG.21: 2 residues within 4Å: Chain B: N.692 Chain C: Y.779 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.692 NAG.22: 2 residues within 4Å: Chain C: Y.12, N.45 No protein-ligand interaction detected (PLIP) NAG.23: 2 residues within 4Å: Chain C: E.264, N.265 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.265 NAG.24: 2 residues within 4Å: Chain C: N.314, Q.563 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.314 NAG.25: 2 residues within 4Å: Chain A: Y.779 Chain C: N.692 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Structure of XBB.1.5 spike/Nanosota-3C complex. To Be Published

Release Date

2024-09-18

Peptides

Spike glycoprotein: ABC
Nanosota-3C: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
L

Spike glycoprotein

Nanosota-3C

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