› 4d6r

X-ray diffraction
1.4Å resolution

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound o-toluenesulfonamide

Released:
DOI: 10.2210/pdb4d6r/pdb
PDB entry 4d6r coloured by chain, front view.
PDB entry 4d6r coloured by chain, side view.
PDB entry 4d6r coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Krojer T, Vollmar M, Bradley A, Crawley L, Szykowska A, Burgess-Brown N, Gileadi C, Johansson C, Oppermann U, Bountra C, Arrowsmith CH, Edwards A, von Delft F

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179409 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4D Chain: A
Molecule details ›
Chain: A
Length: 343 amino acids
Theoretical weight: 39.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6B0I6 (Residues: 1-342; Coverage: 65%)
Gene names: JHDM3D, JMJD2D, KDM4D
Sequence domains:
Structure domains: Cupin

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand NI 1 x NI
Ligand EDO 4 x EDO
Ligand OGA 1 x OGA
Ligand IEJ 3 x IEJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P43212
Unit cell:
a: 71.514Å b: 71.514Å c: 150.42Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.146 0.145 0.172
Expression system: Escherichia coli

Quick links