› 5bvp

X-ray diffraction
2.2Å resolution

The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta

Released:
DOI: 10.2210/pdb5bvp/pdb
PDB entry 5bvp coloured by chain, front view.
PDB entry 5bvp coloured by chain, side view.
PDB entry 5bvp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1β.
Rondeau JM, Ramage P, Zurini M, Gram H
MAbs 7 1151-60 (2015)
PMID: 26284424

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208442 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
canakinumab Fab heavy-chain Chain: H
Molecule details ›
Chain: H
Length: 225 amino acids
Theoretical weight: 24.18 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
Structure domains: Immunoglobulins
Interleukin-1 beta Chain: I
Molecule details ›
Chain: I
Length: 153 amino acids
Theoretical weight: 17.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01584 (Residues: 117-269; Coverage: 57%)
Gene names: IL1B, IL1F2
Sequence domains: Interleukin-1 / 18
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Canakinumab Fab light-chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.38 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand CL 2 x CL
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 50.928Å b: 56.285Å c: 191.704Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.231
Expression systems:
  • Mus musculus
  • Escherichia coli BL21(DE3)

Quick links

Citations

12 review citations

Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection.
Hwang et al. (2022)
11 more

6 mentions without citation

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.
Jespersen et al. (2017)
5 more