SMTL ID : 9atr.1

local refinement of XBB.1.5 spike/Nanosota-8 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 2 residues within 4Å: Chain C: Y.12, N.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.12

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

NAG.2: 2 residues within 4Å: Chain A: Y.12, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.3: 3 residues within 4Å: Chain A: N.263, E.264, N.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.264 NAG.4: 2 residues within 4Å: Chain B: Y.12, N.45 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.45 NAG.5: 4 residues within 4Å: Chain B: N.106, T.108, N.109, V.111 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.108 Hydrogen bonds: B:T.108, B:N.109 NAG.6: 2 residues within 4Å: Chain B: N.147, N.148 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: K.541 Chain B: N.263, E.264, N.265 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.264, A:K.541 NAG.8: 2 residues within 4Å: Chain B: N.314, Q.563 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.314, B:Q.563 NAG.9: 5 residues within 4Å: Chain B: R.440, K.441, E.448 Chain C: T.92, N.217 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.440, B:K.441, B:K.441, B:E.448

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2025-08-27

Peptides

Spike glycoprotein: ABC
Nanosota-8: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
E

F
H

Spike glycoprotein

Nanosota-8

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