SMTL ID : 8fxb.1

SARS-CoV-2 XBB.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: 6 residues within 4Å: Chain A: Y.50 Chain B: D.115 Chain D: H.30, F.33, N.34, V.58 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.33 Hydrogen bonds: D:N.34

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

NAG.2: 2 residues within 4Å: Chain C: N.72, T.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.72 NAG.3: 4 residues within 4Å: Chain C: N.35, T.37, E.39, Q.322 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.35, C:E.39, C:E.39 NAG.4: 3 residues within 4Å: Chain C: S.402, S.527, N.528 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.402, C:S.402, C:N.528 NAG.5: 4 residues within 4Å: Chain C: V.298, L.302, P.303, N.304 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.298 Hydrogen bonds: C:N.304 NAG.6: 4 residues within 4Å: Chain C: Q.63, N.85, A.175, N.176 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.63

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

Related Entries With Identical Sequence