SMTL ID : 7xb0.1

Crystal structure of Omicron BA.2 RBD complexed with hACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

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.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.83

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: F.267, N.414, W.576 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain B: F.6, D.7, F.10, N.11, V.35, L.36, Y.37, F.39 No protein-ligand interaction detected (PLIP)

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

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

NAG.5: 4 residues within 4Å: Chain A: N.35, T.37, E.39, Q.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.35, A:E.39 NAG.6: 2 residues within 4Å: Chain A: V.298, N.304 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.298 Hydrogen bonds: A:N.304 NAG.7: 4 residues within 4Å: Chain A: S.402, D.525, S.527, N.528 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:S.402, A:N.528

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
A

B
B

Angiotensin-converting enzyme 2

Spike protein S1

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