› 4c8d

X-ray diffraction
2.18Å resolution

Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)

Released:
DOI: 10.2210/pdb4c8d/pdb
PDB entry 4c8d coloured by chain, front view.
PDB entry 4c8d coloured by chain, side view.
PDB entry 4c8d coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Vollmar M, Johansson C, Gileadi C, Goubin S, Szykowska A, Krojer T, Crawley L, von Delft F, Arrowsmith CH, Bountra C, Edwards A, Oppermann U

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181640 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 3B Chain: A
Molecule details ›
Chain: A
Length: 349 amino acids
Theoretical weight: 40.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7LBC6 (Residues: 1380-1720; Coverage: 19%)
Gene names: C5orf7, JHDM2B, JMJD1B, KDM3B, KIAA1082
Sequence domains: JmjC domain, hydroxylase
Structure domains: Cupin

Ligands and Environments

5 bound ligands:
Ligand MN 1 x MN
Ligand OGA 1 x OGA
Ligand GOL 1 x GOL
Ligand ACT 2 x ACT
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: I222
Unit cell:
a: 83.34Å b: 85.61Å c: 117.13Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.194 0.239
Expression system: Escherichia coli BL21(DE3)

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