SMTL ID : 7wjy.1

Omicron spike trimer with 6m6 antibody

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.706 Chain G: Y.793 Ligand excluded by PLIP NAG.4: 5 residues within 4Å: Chain A: T.713, N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: I.1129, N.1131 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain D: T.106, N.231, T.233 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain D: N.277, E.278, N.279 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain D: N.328, Q.577 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain D: N.613 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: Y.793 Chain D: Y.704, S.705, N.706 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain D: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.798, S.800 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain D: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: I.1129, V.1130, N.1131 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain G: N.277, E.278, N.279 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain G: N.328, P.576, Q.577, T.578, L.579 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain G: N.613, Q.641 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: I.791, Y.793 Chain G: S.705, N.706 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain G: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain G: N.798, S.800 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain G: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain G: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding. Cell Res. (2022)

Release Date

2022-07-13

Peptides

Spike glycoprotein: ADG
6m6 heavy chain: BE
6m6 light chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

B
B

E
E

C
C

F
F

Spike glycoprotein

6m6 heavy chain

6m6 light chain

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