SMTL ID : 7wly.1

Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down- and 2 up RBDs)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: I.465 Chain C: N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: K.455, S.456, N.457 Chain C: T.106, N.231, T.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.455, A:S.456

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

NAG.3: 2 residues within 4Å: Chain A: E.278, N.279 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.328, I.329, Q.577 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain C: I.831, Q.833 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.706, I.1127 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.714, F.715, Q.923 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Q.833 Chain B: N.613, T.615 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.714 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.798, Q.801 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1071 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.328, I.329, Q.577 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Q.833 Chain C: N.613 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: Y.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.714, Q.1068 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Q.892 Chain C: E.1069, N.1071 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.1095, H.1098, F.1100 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., 35B5 antibody potently neutralizes SARS-CoV-2 Omicron by disrupting the N-glycan switch via a conserved spike epitope. Cell Host Microbe (2022)

Release Date

2022-05-25

Peptides

Spike glycoprotein: ABC
Heavy chain of 35B5 Fab: DF
Light chain of 35B5 Fab: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
P

F
Y

E
O

G
X

Spike glycoprotein

Heavy chain of 35B5 Fab

Light chain of 35B5 Fab

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