SMTL ID : 7zf7.1

SARS-CoV-2 Omicron BA.2 RBD in complex with ACE2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.46 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.304, M.305, T.306, Q.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.2: 3 residues within 4Å: Chain A: S.402, D.525, N.528 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:N.528 NAG.3: 3 residues within 4Å: Chain A: F.267, N.414, W.576 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.267 Hydrogen bonds: A:N.414 NAG.4: 3 residues within 4Å: Chain A: N.35, T.37, Q.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.35 NAG.5: 2 residues within 4Å: Chain A: K.8, N.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.8 NAG.6: 4 residues within 4Å: Chain A: Q.63, N.85, N.176, H.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85, A:H.177

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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

Nutalai, R. et al., Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell (2022)

Release Date

2022-06-01

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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