SMTL ID : 7t9l.1

Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: F.335, D.336, F.339, N.340, V.364, L.368, F.371 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.339 Hydrogen bonds: A:D.336 NAG.2: 3 residues within 4Å: Chain B: N.36, E.40, Q.323 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.36, B:T.38, B:E.40, B:Q.323 NAG.3: 3 residues within 4Å: Chain B: K.9, N.73, T.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.75 NAG.4: 5 residues within 4Å: Chain B: Q.64, Q.84, N.86, V.90, H.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.84, B:N.86 NAG.5: 4 residues within 4Å: Chain B: E.295, N.305, M.306, W.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.305 NAG.6: 3 residues within 4Å: Chain B: F.268, N.415, W.577 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.268 NAG.7: 2 residues within 4Å: Chain B: S.403, N.529 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.403, B:S.403, B:S.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science (2022)

Release Date

2021-12-29

Peptides

Spike glycoprotein: A
Processed angiotensin-converting enzyme 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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