PDBe 5fza

X-ray diffraction
2.1Å resolution

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-piperidin-4-yloxy-5-(trifluoromethyl)pyridine (N10072a) (ligand modelled based on PANDDA event map)

Source organism: Homo sapiens
Entry authors: Nowak R, Krojer T, Pearce N, Johansson C, Gileadi C, Kupinska K, Strain-Damerell C, Szykowska A, Burgess-Brown NA, Arrowsmith CH, Bountra C, Edwards AM, von Delft F, Brennan PE, Oppermann U

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Lysine-specific demethylase 5B Chain: A
Molecule details ›
Chain: A
Length: 479 amino acids
Theoretical weight: 55.21 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
  • Canonical: Q9UGL1 (Residues: 26-101, 374-770; Coverage: 31%)
  • Best match: Q9UGL1-2 (Residues: 410-806)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
Sequence domains:
Structure domains: Cupin

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6522
Unit cell:
a: 141.37Å b: 141.37Å c: 153.105Å
α: 90° β: 90° γ: 120°
R R work R free
0.194 0.193 0.228
Expression system: Spodoptera frugiperda