SMTL ID : 7tlz.1

SARS-CoV-2 S NTD B.1.1.529 Omicron variant + S309 Local Refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain C: E.130, N.159, N.160 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain C: N.277, N.279 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.279 NAG.3: 2 residues within 4Å: Chain C: C.15, N.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.15 NAG.4: 3 residues within 4Å: Chain A: R.30 Chain B: R.103 Chain C: N.231 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:R.103, A:R.30, C:N.231 NAG.5: 2 residues within 4Å: Chain C: Y.28, N.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.28 NAG.6: 2 residues within 4Å: Chain C: N.120, V.125 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science (2022)

Release Date

2022-02-02

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
J

S2L20 Fab light chain

S2L20 Fab heavy chain

Spike glycoprotein

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