SMTL ID : 8xn2.1

SARS-CoV-2 Omicron EG.5.1 RBD in complex with human ACE2 (local refined from the spike protein)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: K.8, N.72 Chain B: T.97 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.322 Hydrogen bonds: A:Q.322 NAG.3: 3 residues within 4Å: Chain A: Q.63, Q.83, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:Q.83 NAG.4: 3 residues within 4Å: Chain A: D.413, N.414, E.415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.414 NAG.5: 1 residues within 4Å: Chain A: N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.528 NAG.6: 1 residues within 4Å: Chain A: N.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure (2024)

Release Date

2024-07-03

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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