PDBe 5fzm

X-ray diffraction
2.49Å resolution

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid (N09989b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Source organism: Homo sapiens
Entry authors: Nowak R, Krojer T, Johansson C, Kupinska K, Szykowska A, Pearce N, Talon R, Collins P, Gileadi C, Strain-Damerell C, 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: 55.14 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
  • Canonical: Q9UGL1 (Residues: 26-101, 376-770; Coverage: 31%)
  • Best match: Q9UGL1-2 (Residues: 412-806)
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 I04-1
Spacegroup: P6522
Unit cell:
a: 141.88Å b: 141.88Å c: 151.61Å
α: 90° β: 90° γ: 120°
R R work R free
0.185 0.183 0.224
Expression system: Spodoptera frugiperda