SMTL ID : 8s9g.1

SARS-CoV-2 BN.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- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-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-MAN-FUC.1: 9 residues within 4Å: Chain B: H.31, F.34, N.35, V.59 Chain C: R.98, Y.100, G.112, D.115 Chain D: Y.50 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.100, D:Y.50 Hydrogen bonds: C:R.98, C:R.98

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

NAG.2: 1 residues within 4Å: Chain A: N.72 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: N.35, E.39, N.40 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: V.298, L.302, P.303, N.304 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.298 NAG.5: 5 residues within 4Å: Chain A: Q.63, Q.83, N.85, A.175, N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:N.85 NAG.6: 3 residues within 4Å: Chain B: F.39, A.40, N.46 No protein-ligand interaction detected (PLIP)

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
H

D
L

Processed angiotensin-converting enzyme 2

Spike glycoprotein

S309 Fab Heavy chain

S309 Fab Light chain

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