› 5lw9

X-ray diffraction
2.3Å resolution

Crystal structure of human JARID1B in complex with S40563a

Released:
DOI: 10.2210/pdb5lw9/pdb
PDB entry 5lw9 coloured by chain, front view.
PDB entry 5lw9 coloured by chain, side view.
PDB entry 5lw9 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Srikannathasan V, Le Bihan YV, Szykowska A, Johansson C, Gileadi C, Arrowsmith CH, Edwards AM, Bountra C, von Delft F, Oppermann U, Huber K

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: 26-99, 374-772; Coverage: 31%)
  • Best match: Q9UGL1-2 (Residues: 374-403, 410-808)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
Sequence domains:
Structure domains: Cupin

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand MN 2 x MN
Ligand EDO 2 x EDO
Ligand DMS 3 x DMS
Ligand 5UJ 1 x 5UJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P6522
Unit cell:
a: 142.96Å b: 142.96Å c: 152.47Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.185 0.218
Expression system: Spodoptera frugiperda

Quick links