SMTL ID : 8xuu.1

BA.2.86-T356K Spike Trimer in complex with heparan sulfate (Local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

NAG-BMA.1: 2 residues within 4Å: Chain A: N.279, N.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.279

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

NAG.2: 7 residues within 4Å: Chain A: N.123, A.124, T.125, N.126, V.127, F.128, V.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.123, A:T.125, A:N.126 NAG.3: 3 residues within 4Å: Chain A: F.341, N.342, F.370 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.164, N.165 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.164 Hydrogen bonds: A:N.164, A:N.165 NAG.5: 3 residues within 4Å: Chain A: T.109, N.233, E.464 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.109, A:E.464, A:E.464 NAG.6: 2 residues within 4Å: Chain A: P.329, N.330 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.329 NAG.8: 2 residues within 4Å: Chain A: Y.31, N.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.31, A:N.64

1 x IDU: 2-O-sulfo-beta-L-altropyranuronic acid(Non-covalent)

IDU.7: 5 residues within 4Å: Chain A: F.168, Y.170, R.354, K.355, R.356 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.170, A:R.354, A:R.356, A:R.356 Salt bridges: A:R.354, A:R.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, P. et al., Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity. Natl Sci Rev (2024)

Release Date

2024-07-03

Peptides

Spike glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike glycoprotein

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