› 5fjk

X-ray diffraction
1.66Å resolution

Crystal structure of human JMJD2C catalytic domain in complex 6-ethyl- 5-methyl-7-oxo-4,7-dihydropyrazolo(1,5-a)pyrimidine-3-carbonitrile

Released:
DOI: 10.2210/pdb5fjk/pdb
PDB entry 5fjk coloured by chain, front view.
PDB entry 5fjk coloured by chain, side view.
PDB entry 5fjk coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Cecatiello V, Pasqualato S

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190586 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4C Chain: A
Molecule details ›
Chain: A
Length: 349 amino acids
Theoretical weight: 40.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H3R0 (Residues: 3-347; Coverage: 33%)
Gene names: GASC1, JHDM3C, JMJD2C, KDM4C, KIAA0780
Sequence domains:
Structure domains: Cupin

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand NI 1 x NI
Ligand EM6 1 x EM6
Ligand CL 4 x CL
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2221
Unit cell:
a: 89.9Å b: 91.27Å c: 98.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.197
Expression system: Escherichia coli BL21(DE3)

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