SMTL ID : 7wbp.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor human ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: 5 residues within 4Å: Chain A: W.51, L.55, Q.84, N.85, Y.184 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 Hydrogen bonds: A:N.35, A:E.39 NAG.3: 2 residues within 4Å: Chain A: K.8, N.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.8 NAG.4: 2 residues within 4Å: Chain A: N.304, M.305 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, E.415 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.267, A:E.415 NAG.7: 5 residues within 4Å: Chain B: F.20, D.21, F.24, N.25, N.52 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.20, B:F.24 Hydrogen bonds: B:N.25, B:N.52

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, P. et al., Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell (2022)

Release Date

2022-01-19

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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