SMTL ID : 8fxc.1

SARS-CoV-2 BQ.1.1 spike RBD bound to the human ACE2 ectodomain and the S309 neutralizing antibody Fab fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 7 residues within 4Å: Chain A: Y.50 Chain B: R.98, Y.100, D.115 Chain D: F.33, N.34, F.62 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:Y.32, B:R.98, B:D.115 Hydrophobic interactions: A:Y.50, D:F.33

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

NAG.2: 1 residues within 4Å: Chain C: N.72 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain C: N.35, T.37, Q.322 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain C: N.304 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain C: Q.63, N.85, N.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.63, C:N.85 NAG.6: 2 residues within 4Å: Chain C: S.402, N.528 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain C: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.356, C:H.360, C:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Addetia, A. et al., Neutralization, effector function and immune imprinting of Omicron variants. Nature (2023)

Release Date

2023-10-04

Peptides

S309 Light chain: A
S309 Heavy chain: B
Processed angiotensin-converting enzyme 2: C
Spike protein S1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

D
E

S309 Light chain

S309 Heavy chain

Processed angiotensin-converting enzyme 2

Spike protein S1

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