SMTL ID : 7xb1.1

Crystal structure of Omicron BA.3 RBD complexed with hACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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)

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.2: 9 residues within 4Å: Chain A: W.51, L.55, Q.84, N.85, Y.184, F.372, L.373, N.376, Y.492 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.373

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.3: 8 residues within 4Å: Chain B: F.6, D.7, F.10, N.11, S.34, V.35, Y.37, F.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.34, B:Y.37

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: 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:E.39, A:N.40 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: F.267, N.414, I.418, W.576 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.267, A:I.418 Hydrogen bonds: A:N.414

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

Related Entries With Identical Sequence