SMTL ID : 7ya1.1

Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (local refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

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: 3 residues within 4Å: Chain B: D.7, F.10, N.11 No protein-ligand interaction detected (PLIP)

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

NAG.2: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, Q.322 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.35, A:E.39, A:E.39, A:N.40 NAG.3: 2 residues within 4Å: Chain A: K.8, N.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.72 NAG.4: 2 residues within 4Å: Chain A: N.304, M.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.305 NAG.5: 4 residues within 4Å: Chain A: F.267, N.414, E.415, W.576 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.267 Hydrogen bonds: A:N.414, A:E.415 NAG.6: 2 residues within 4Å: Chain A: S.402, N.528 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.402, A:S.402

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.356, H.360, E.384 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.356, A:H.356, A:H.360, A:E.384, A:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Angiotensin-converting enzyme 2

Spike protein S1

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