SMTL ID : 7sod.1

SARS-CoV-2 S NTD B.1.617.1 kappa variant S2L20 Local Refinement

Coordinates

PDB Format

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: 4 residues within 4Å: Chain C: N.122, A.123, T.124, V.127 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain C: F.59, N.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.61 NAG.3: 4 residues within 4Å: Chain A: R.30, Y.32 Chain B: R.103 Chain C: N.234 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:R.30, A:R.30, A:Y.32, B:R.103, C:N.234 NAG.4: 3 residues within 4Å: Chain C: N.280, E.281, N.282 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.281, C:N.282 NAG.5: 2 residues within 4Å: Chain C: C.15, N.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.15, C:N.17 NAG.6: 2 residues within 4Å: Chain C: N.164, N.165 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.164 Hydrogen bonds: C:N.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science (2021)

Release Date

2021-11-17

Peptides

S2L20 Fab light chain: A
S2L20 Fab heavy chain: B
Spike glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

S2L20 Fab light chain

S2L20 Fab heavy chain

Spike glycoprotein

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