SMTL ID : 7yvu.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.35, R.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.322 NAG.2: 5 residues within 4Å: Chain A: E.292, K.295, S.402, I.403, N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.292 NAG.4: 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:D.7

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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

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

Processed angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Processed angiotensin-converting enzyme 2

Spike protein S1

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