SMTL ID : 7wti.1

SARS-CoV-2 Omicron variant spike in complex with Fab XGv264

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: T.106, T.112, N.231 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: E.278, N.279 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: F.335, D.336, N.340, V.364 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.714, Q.1068 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.798 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: E.1069, N.1071 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: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.231, T.233 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: F.339, N.340, L.368 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: I.791 Chain B: N.706 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1071 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: I.1129, V.1130, N.1131 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: F.84, N.231, T.233, R.234 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: N.328, I.329, Q.577, T.578, L.579 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: D.336, F.339, N.340 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.714 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1071 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.36: 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, L. et al., Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages. Cell Res. (2022)

Release Date

2022-12-21

Peptides

Spike glycoprotein: ABC
Heavy chain of XGv264: DEH
Light chain of XGv264: FGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
I

H
G

F
K

G
L

I
J

Spike glycoprotein

Heavy chain of XGv264

Light chain of XGv264

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