SMTL ID : 8d0z.1

S728-1157 IgG in complex with SARS-CoV-2-6P-Mut7 Spike protein (focused refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: T.716, N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG.2: 3 residues within 4Å: Chain A: K.795, N.801, S.803 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.801 NAG.3: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.580 NAG.5: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.338, B:F.342, B:L.368 NAG.6: 3 residues within 4Å: Chain B: K.795, N.801, S.803 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.801, B:S.803, B:Q.804 NAG.7: 1 residues within 4Å: Chain B: N.717 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.717, B:Q.926 NAG.8: 2 residues within 4Å: Chain C: T.716, N.717 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain C: K.795, D.796, N.801, S.803 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.795 NAG.10: 4 residues within 4Å: Chain C: N.1098, G.1099, T.1100, F.1103 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.1100 Hydrogen bonds: C:T.1100 NAG.11: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.580

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Changrob, S. et al., Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants. J.Clin.Invest. (2023)

Release Date

2023-03-22

Peptides

Spike glycoprotein: ABC
S728-1157 Fab heavy chain variable region: D
S728-1157 Fab light chain variable region: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
H

E
L

Spike glycoprotein

S728-1157 Fab heavy chain variable region

S728-1157 Fab light chain variable region

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