SMTL ID : 8h06.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with human ACE2 (local refinement)

Coordinates

PDB Format Compare

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: 4 residues within 4Å: Chain A: Q.63, Q.83, N.85, H.177 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 2 residues within 4Å: Chain A: S.402, N.528 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: N.35, T.37, V.321, Q.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.37 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: 1 residues within 4Å: Chain A: N.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.6: 3 residues within 4Å: Chain A: F.267, N.414, W.576 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.267 NAG.8: 3 residues within 4Å: Chain B: N.11, N.38, F.39 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.38, B:F.39

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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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