SMTL ID : 7xcp.1

Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-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: 5 residues within 4Å: Chain A: W.51, L.55, Q.84, N.85, Y.184 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.35, 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:K.8 NAG.4: 3 residues within 4Å: Chain A: V.298, N.304 Chain C: R.86 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.86, C:R.86 NAG.6: 2 residues within 4Å: Chain A: N.414, W.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.414 NAG.7: 4 residues within 4Å: Chain B: D.7, F.10, N.11, L.39 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.10 Hydrogen bonds: B:N.11

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.356, A:H.360, 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

Processed angiotensin-converting enzyme 2: A
Spike protein S1: B
Heavy chain of 304 Fab: C
Lignt chain of 304 Fab: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Processed angiotensin-converting enzyme 2

Spike protein S1

Heavy chain of 304 Fab

Lignt chain of 304 Fab

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