PDBe 4d6s

X-ray diffraction
1.4Å resolution

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound 5,6-Dimethylbenzimidazole

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

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
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
  • Canonical: Q6B0I6 (Residues: 1-342; Coverage: 65%)
Gene names: JHDM3D, JMJD2D, KDM4D
Sequence domains:
Structure domains: Cupin

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 71.225Å b: 71.225Å c: 150.208Å
α: 90° β: 90° γ: 90°
R R work R free
0.14 0.139 0.164
Expression system: Escherichia coli