› 5fzk

X-ray diffraction
2.05Å resolution

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Released:
DOI: 10.2210/pdb5fzk/pdb
PDB entry 5fzk coloured by chain, front view.
PDB entry 5fzk coloured by chain, side view.
PDB entry 5fzk coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Nowak R, Krojer T, Johansson C, Gileadi C, Kupinska K, Strain-Damerell C, Szykowska A, Talon R, Collins P, Burgess-Brown NA, Arrowsmith CH, Bountra C, Edwards AM, von Delft F, Brennan PE, Oppermann U

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: 479 amino acids
Theoretical weight: 55.21 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • 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

7 bound ligands:
Ligand ZN 1 x ZN
Ligand CL 1 x CL
Ligand MN 1 x MN
Ligand EDO 9 x EDO
Ligand NRW 1 x NRW
Ligand PO4 1 x PO4
Ligand DMS 2 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P6522
Unit cell:
a: 142.05Å b: 142.05Å c: 152.13Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.204 0.238
Expression system: Spodoptera frugiperda

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