SMTL ID : 8h5c.1

Structure of SARS-CoV-2 Omicron BA.2.75 RBD in complex with human ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

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: 1 residues within 4Å: Chain A: N.72 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: 7 residues within 4Å: Chain A: W.51, N.85, Y.184, F.372, L.373, N.376, Y.492 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.373 Hydrogen bonds: A:N.376

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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

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

NAG.4: 3 residues within 4Å: Chain A: N.35, T.37, Q.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.35, A:Q.322 NAG.5: 1 residues within 4Å: Chain A: N.304 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: F.267, N.414, W.576 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.267 Hydrogen bonds: A:N.414

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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