SMTL ID : 7xaz.2 (1 other biounit)

Crystal structure of Omicron BA.1.1 RBD complexed with hACE2

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: 2 residues within 4Å: Chain A: K.8, N.72 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.35, A:E.39, A:N.40 NAG.3: 2 residues within 4Å: Chain A: N.304, M.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.5: 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.6: 4 residues within 4Å: Chain A: S.402, D.525, S.527, N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.402 NAG.7: 6 residues within 4Å: Chain B: F.6, F.10, N.11, V.35, L.36, N.38 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.6, B:F.10, B:L.36 Hydrogen bonds: B:D.7, B:N.11, B:V.35, B:N.38

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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

Li, L. et al., Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell (2022)

Release Date

2022-07-06

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Angiotensin-converting enzyme 2

Spike protein S1

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