SMTL ID : 7yj3.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with human 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: 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

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

NAG.2: 4 residues within 4Å: Chain A: F.267, N.414, E.415, I.418 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.267, A:E.415, A:I.418 NAG.3: 2 residues within 4Å: Chain A: N.35, Q.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.35 NAG.4: 1 residues within 4Å: Chain A: N.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.72 NAG.5: 2 residues within 4Å: Chain A: Q.63, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:N.176 NAG.6: 3 residues within 4Å: Chain A: S.402, D.525, N.528 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:N.528 NAG.7: 1 residues within 4Å: Chain A: N.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.8: 4 residues within 4Å: Chain B: D.7, N.11, N.38, F.39 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.39 Hydrogen bonds: B:N.11

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 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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