SMTL ID : 7soc.1

SARS-CoV-2 S RBD B.1.617.1 kappa variant S309 Local Refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 13 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, L.368 Chain B: R.98, Y.100, I.111, G.112, D.115 Chain C: Y.49, T.56 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.49, B:Y.100 Hydrogen bonds: C:T.56, B:R.98, B:D.115, B:D.115, C:T.56

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

NAG.2: 2 residues within 4Å: Chain A: P.330, N.331 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.330

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

Spike glycoprotein: A
S309 Fab heavy chain: B
S309 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

S309 Fab heavy chain

S309 Fab light chain

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