SMTL ID : 8dm2.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein (focused refinement of NTD)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

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: 5 residues within 4Å: Chain A: N.119, T.121, N.122, V.124, E.151 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: Y.25, N.58 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.162 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: T.105, N.231, T.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.231 NAG.5: 3 residues within 4Å: Chain A: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep (2023)

Release Date

2023-01-25

Peptides

Spike glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike glycoprotein

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