› 5fv3

X-ray diffraction
2.37Å resolution

Crystal structure of human JARID1B construct c2 in complex with N- Oxalylglycine.

Released:
DOI: 10.2210/pdb5fv3/pdb
PDB entry 5fv3 coloured by chain, front view.
PDB entry 5fv3 coloured by chain, side view.
PDB entry 5fv3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of human KDM5B guides histone demethylase inhibitor development.
Johansson C, Velupillai S, Tumber A, Szykowska A, Hookway ES, Nowak RP, Strain-Damerell C, Gileadi C, Philpott M, Burgess-Brown N, Wu N, Kopec J, Nuzzi A, Steuber H, Egner U, Badock V, Munro S, LaThangue NB, Westaway S, Brown J, Athanasou N, Prinjha R, Brennan PE, Oppermann U
Nat Chem Biol 12 539-45 (2016)
PMID: 27214403

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: 484 amino acids
Theoretical weight: 55.75 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UGL1 (Residues: 26-101, 369-770; Coverage: 31%)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
Sequence domains:
Structure domains: Cupin

Ligands and Environments

7 bound ligands:
Ligand ZN 1 x ZN
Ligand DMS 2 x DMS
Ligand MN 2 x MN
Ligand EPE 1 x EPE
Ligand EDO 9 x EDO
Ligand CL 1 x CL
Ligand OGA 1 x OGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P6522
Unit cell:
a: 142.35Å b: 142.35Å c: 152.33Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.196 0.194 0.235
Expression system: Spodoptera frugiperda

Quick links

Citations

25 review citations

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