SMTL ID : 7yv8.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384

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

NAG.2: 2 residues within 4Å: Chain A: N.72, T.74 No protein-ligand interaction detected (PLIP) NAG.3: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, R.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.39 NAG.4: 2 residues within 4Å: Chain A: N.64 Chain B: F.155 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.414, W.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.414 NAG.6: 4 residues within 4Å: Chain A: S.402, D.525, S.527, N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.402 NAG.7: 2 residues within 4Å: Chain B: N.12, F.40 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants. Nat Commun (2023)

Release Date

2023-07-19

Peptides

Angiotensin-converting enzyme: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Angiotensin-converting enzyme

Spike glycoprotein

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