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

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.36 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: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, Q.322 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 6 residues within 4Å: Chain A: K.8, N.72 Chain B: Q.98, T.104, G.105, N.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.104, B:Q.98, B:N.106

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.3: 2 residues within 4Å: Chain A: V.298, N.304 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN.4: 3 residues within 4Å: Chain A: S.402, D.525, N.528 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:E.357, A:H.360, A:E.384

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

NAG.6: 3 residues within 4Å: Chain A: Q.63, Q.83, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:Q.63 NAG.7: 2 residues within 4Å: Chain A: N.414, W.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimura, I. et al., Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell (2022)

Release Date

2022-09-28

Peptides

Processed angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Processed angiotensin-converting enzyme 2

Spike protein S1

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