SMTL ID : 7wsk.1

Crystal structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with civet ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 4 residues within 4Å: Chain A: N.36, T.38, E.40, N.41 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.40

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

NAG.2: 4 residues within 4Å: Chain A: N.199, Y.200, S.201, Q.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.201 NAG.3: 2 residues within 4Å: Chain A: V.299, N.305 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: T.403, D.526, S.528, N.529 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.403 Hydrogen bonds: A:T.403 NAG.6: 5 residues within 4Å: Chain B: F.20, D.21, F.24, N.25, V.49 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.24 Hydrogen bonds: B:N.25, B:V.49

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.357, E.358, H.361, E.385 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.357, A:H.361, A:E.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s. Cell Discov (2022)

Release Date

2022-06-08

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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