› 7shu

X-ray diffraction
2.75Å resolution

IgE-Fc in complex with omalizumab variant C02

Released:
DOI: 10.2210/pdb7shu/pdb
PDB entry 7shu coloured by chain, front view.
PDB entry 7shu coloured by chain, side view.
PDB entry 7shu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex.
Pennington LF, Gasser P, Kleinboelting S, Zhang C, Skiniotis G, Eggel A, Jardetzky TS
OpenAccess logo Nat Commun 12 7069 (2021)
PMID: 34862384

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-525442 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
omalizumab variant C02 VH Chains: C, E
Molecule details ›
Chains: C, E
Length: 123 amino acids
Theoretical weight: 13.44 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
omalizumab variant C02 VL Chains: D, F
Molecule details ›
Chains: D, F
Length: 134 amino acids
Theoretical weight: 14.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Immunoglobulin heavy constant epsilon Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 24.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01854 (Residues: 209-426; Coverage: 40%)
Gene name: IGHE
Sequence domains: Immunoglobulin C1-set domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 1 x NAG
Ligand EDO 1 x EDO
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 90.07Å b: 176.12Å c: 142.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.275
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Accelerating therapeutic protein design with computational approaches toward the clinical stage.
Chen et al. (2023)
1 more