SMTL ID : 8vyf.1

SARS-CoV-2 S NTD (C.37 Lambda variant) plus S2L20 and S2X303 Fabs, local refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: N.122, A.123, T.124, V.127 Chain D: F.104 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.234 Chain C: R.30 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: F.59, N.61 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: N.273, E.274, N.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.273 NAG.5: 1 residues within 4Å: Chain A: N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165 NAG.6: 2 residues within 4Å: Chain A: N.148, N.149 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.148 Hydrogen bonds: A:N.149 NAG.7: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: R.158, N.246, W.251 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.251 Hydrogen bonds: A:N.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magaret, C.A. et al., Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. Nat Commun (2024)

Release Date

2024-03-27

Peptides

Spike glycoprotein: A
S2L20 Heavy Chain: B
S2L20 Light Chain: C
S2X303 Heavy Chain: D
S2X303 Light Chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

S2L20 Heavy Chain

S2L20 Light Chain

S2X303 Heavy Chain

S2X303 Light Chain

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