SMTL ID : 8f0g.1

Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-mer

Ligands

3 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: 6 residues within 4Å: Chain C: N.124, T.126, N.127, V.129, E.168, V.170 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.170 NAG-NAG.2: 8 residues within 4Å: Chain C: N.235, T.237 Chain E: R.458, K.459, S.460, L.462, K.463, E.466 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.459 NAG-NAG.3: 3 residues within 4Å: Chain E: N.802, S.804, Q.805 No protein-ligand interaction detected (PLIP)

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

NAG.4: 6 residues within 4Å: Chain C: S.114, E.134, N.163, N.164 Chain E: Y.352, T.471 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain C: Y.32, N.65, P.632 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain C: N.332, Q.581, T.582 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain C: N.281, E.282, N.283 Chain E: K.559 Ligand excluded by PLIP NAG.8: 6 residues within 4Å: Chain C: N.718, F.719, T.720, L.923, Q.927, Q.1072 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain C: N.802, S.804, Q.805 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain C: N.710, N.711 Chain D: I.795, Y.797 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain C: E.1073, N.1075 Chain D: A.894, Q.896 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain C: N.1099, T.1101, H.1102, F.1104 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain D: N.802, S.804 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.718, L.923 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain D: N.710 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: N.1099, H.1102, F.1104 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain D: N.1135 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: Y.797 Chain E: N.710 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain E: N.718, L.923, Q.927 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain E: F.343, N.344, V.368, N.371 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain E: N.617, Q.645 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hastie, K.M. et al., Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence. Cell Rep (2023)

Release Date

2023-05-03

Peptides

Antibody 1C3 Fab Heavy Chain: A
Antibody 1C3 Fab Light Chain: B
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
Y

C
A

D
B

E
C

Antibody 1C3 Fab Heavy Chain

Antibody 1C3 Fab Light Chain

Spike glycoprotein