› 5fun

X-ray diffraction
2.3Å resolution

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5B Chain: A
Molecule details ›
Chain: A
Length: 481 amino acids
Theoretical weight: 55.46 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UGL1 (Residues: 26-101, 374-772; Coverage: 31%)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
Sequence domains:
Structure domains: Cupin

Ligands and Environments

7 bound ligands:
Ligand ZN 2 x ZN
Ligand GZA 1 x GZA
Ligand MN 1 x MN
Ligand NA 1 x NA
Ligand PO4 1 x PO4
Ligand EPE 1 x EPE
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P6522
Unit cell:
a: 142.842Å b: 142.842Å c: 152.011Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.18 0.212
Expression system: Spodoptera frugiperda

Quick links

Citations

23 review citations

The great escape: tumour cell plasticity in resistance to targeted therapy.
Boumahdi et al. (2020)
22 more

3 mentions without citation

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
2 more