SMTL ID : 9c45.1

SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-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: 3 residues within 4Å: Chain C: N.122, N.125, V.127 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: R.30 Chain B: R.103 Chain C: N.234 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain C: F.59, N.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.61 NAG.4: 4 residues within 4Å: Chain C: C.15, V.16, N.17, S.254 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.16, C:S.254 Hydrogen bonds: C:C.15 NAG.5: 3 residues within 4Å: Chain C: N.280, E.281, N.282 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.280, C:E.281, C:N.282 NAG.6: 2 residues within 4Å: Chain C: Q.115, N.165 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, P. et al., Design of customized coronavirus receptors. Nature (2024)

Release Date

2024-11-20

Peptides

S2L20 Fab Light Chain Variable Region: A
S2L20 Fab Heavy Chain Variable: B
Spike glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

S2L20 Fab Light Chain Variable Region

S2L20 Fab Heavy Chain Variable

Spike glycoprotein

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