SMTL ID : 8gou.1

Omicron BA.4/5 SARS-CoV-2 S in complex with TH003 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

37 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: Y.796 Chain C: N.709 Ligands: NAG.33 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.709 Ligands: NAG.13 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: Y.796 Ligands: NAG.11 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.709 Ligands: NAG.26 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.796 Ligands: NAG.24 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: S.708, N.709 Ligands: NAG.4 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: S.112, K.113, N.165 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun (2023)

Release Date

2023-06-28

Peptides

Spike glycoprotein: ABC
TH003 Fab heavy chain: DF
TH003 Fab light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
I

F
H

E
J

G
K

Spike glycoprotein

TH003 Fab heavy chain

TH003 Fab light chain

Related Entries With Identical Sequence