› 2xdv

X-ray diffraction
2.57Å resolution

Crystal Structure of the Catalytic Domain of FLJ14393

Released:
DOI: 10.2210/pdb2xdv/pdb
PDB entry 2xdv coloured by chain, front view.
PDB entry 2xdv coloured by chain, side view.
PDB entry 2xdv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JRC, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ
Nature 510 422-426 (2014)
PMID: 24814345

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo hexamer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184850 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal oxygenase 2 Chain: A
Molecule details ›
Chain: A
Length: 442 amino acids
Theoretical weight: 50.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IUF8 (Residues: 26-465; Coverage: 95%)
Gene names: MDIG, MINA, MINA53, NO52, RIOX2
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand OGA 1 x OGA
Ligand NI 6 x NI
Ligand MN 1 x MN
Ligand EDO 2 x EDO
Ligand CD 3 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P4332
Unit cell:
a: 185.18Å b: 185.18Å c: 185.18Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

22 review citations

Histone demethylases in chromatin biology and beyond.
Dimitrova et al. (2015)
21 more

5 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
4 more