› 8xx0

X-ray diffraction
2.9Å resolution

Crystal structure of anti-IgE antibody HMK-12 Fab complexed with IgE F(ab')2

Released:
DOI: 10.2210/pdb8xx0/pdb
PDB entry 8xx0 coloured by chain, front view.
PDB entry 8xx0 coloured by chain, side view.
PDB entry 8xx0 coloured by chain, top view.
Source organisms:
Primary publication:
Allosteric inhibition of IgE-FcεRI interactions by simultaneous targeting of IgE F(ab')2 epitopes.
Hirano T, Koyanagi A, Ago H, Yamamoto M, Kitaura J, Kasai M, Okumura K
Commun Biol 7 1042 (2024)
PMID: 39179708

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-247796 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
anti-IgE antibody HMK-12 Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.6 KDa
Source organism: Rattus norvegicus
anti-IgE antibody HMK-12 Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 225 amino acids
Theoretical weight: 24.37 KDa
Source organism: Rattus norvegicus
SPE7 immunoglobulin E F(ab')2 heavy chain Chain: A
Molecule details ›
Chain: A
Length: 321 amino acids
Theoretical weight: 36.01 KDa
Source organism: Mus musculus
SPE7 immunoglobulin E F(ab')2 light chain Chain: B
Molecule details ›
Chain: B
Length: 215 amino acids
Theoretical weight: 22.98 KDa
Source organism: Mus musculus

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand EDO 9 x EDO
Ligand BOG 1 x BOG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 282.05Å b: 86.09Å c: 56.06Å
α: 90° β: 97.19° γ: 90°
R-values:
R R work R free
0.228 0.225 0.267

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