SMTL ID : 8y6a.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 and S309 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: N.35, T.37, Q.322 Chain D: S.22, R.24, D.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.22, D:S.22

2 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.2: 2 residues within 4Å: Chain A: N.72 Chain B: T.97 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.97 NAG-NAG-BMA.4: 7 residues within 4Å: Chain B: F.20, H.21, F.24, N.25, F.53 Chain C: Y.100 Chain D: Y.50 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.53

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: 5 residues within 4Å: Chain A: K.291, E.294, K.295, V.298, N.304 No protein-ligand interaction detected (PLIP)

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

NAG.5: 8 residues within 4Å: Chain A: Q.63, N.85, S.88, V.89, A.175, N.176, H.177, Y.178 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.89 Hydrogen bonds: A:Q.63, A:V.89, A:N.176, A:H.177 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:S.527 NAG.8: 4 residues within 4Å: Chain B: A.30, N.36, T.38 Chain C: F.106 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.30, B:N.36

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain A: H.356, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure (2024)

Release Date

2024-07-03

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B
heavy chain of S309 Fab: C
light chain of S309 Fab: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Angiotensin-converting enzyme 2

Spike protein S1

heavy chain of S309 Fab

light chain of S309 Fab

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