› 5r8k

X-ray diffraction
1.47Å resolution

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 in complex with INTERLEUKIN-1 BETA

Released:
DOI: 10.2210/pdb5r8k/pdb
PDB entry 5r8k coloured by chain, front view.
PDB entry 5r8k coloured by chain, side view.
PDB entry 5r8k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes.
Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF
J Med Chem 63 7559-7568 (2020)
PMID: 32543856

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-134409 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Interleukin-1 beta Chain: A
Molecule details ›
Chain: A
Length: 153 amino acids
Theoretical weight: 17.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01584 (Residues: 117-269; Coverage: 57%)
Gene names: IL1B, IL1F2
Sequence domains: Interleukin-1 / 18

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand S8D 1 x S8D
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P43
Unit cell:
a: 54.71Å b: 54.71Å c: 75.11Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.209
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Diversity and versatility of p38 kinase signalling in health and disease.
Canovas et al. (2021)
1 more