› 4g6j

X-ray diffraction
2.03Å resolution

Crystal structure of human IL-1beta in complex with the therapeutic antibody binding fragment of canakinumab

Released:
DOI: 10.2210/pdb4g6j/pdb
PDB entry 4g6j coloured by chain, front view.
PDB entry 4g6j coloured by chain, side view.
PDB entry 4g6j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
One target-two different binding modes: structural insights into gevokizumab and canakinumab interactions to interleukin-1β.
Blech M, Peter D, Fischer P, Bauer MM, Hafner M, Zeeb M, Nar H
J Mol Biol 425 94-111 (2013)
PMID: 23041424

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-208440 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Interleukin-1 beta Chain: A
Molecule details ›
Chain: A
Length: 158 amino acids
Theoretical weight: 17.99 KDa
Source organism: Homo sapiens
Expression system: Not provided
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)
heavy chain of antibody binding fragment of canakinumab Chain: H
Molecule details ›
Chain: H
Length: 218 amino acids
Theoretical weight: 23.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
Structure domains: Immunoglobulins
light chain of antibody binding fragment of canakinumab Chain: L
Molecule details ›
Chain: L
Length: 212 amino acids
Theoretical weight: 23.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 81.061Å b: 37.3Å c: 189.418Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.226 0.252
Expression system: Not provided

Quick links

Citations

22 review citations

Targeting the NLRP3 Inflammasome in Severe COVID-19.
Freeman et al. (2020)
21 more

12 mentions without citation

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Vreven et al. (2015)
11 more