SMTL ID : 7qo9.1

SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD and NTD (Local)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: N.120, A.121, T.122, N.123, V.125 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.135, D.136 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: T.106, N.231, T.233 Chain B: K.459 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.459, B:K.459 NAG.5: 2 residues within 4Å: Chain A: E.278, N.279 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, D. et al., Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion. Biorxiv (2021)

Release Date

2022-01-26

Peptides

Spike glycoprotein,SARS-CoV-2 S Omicron Spike B.1.1.529: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike glycoprotein,SARS-CoV-2 S Omicron Spike B.1.1.529

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