› 4lxl

X-ray diffraction
1.87Å resolution

Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3

Released:
DOI: 10.2210/pdb4lxl/pdb
PDB entry 4lxl coloured by chain, front view.
PDB entry 4lxl coloured by chain, side view.
PDB entry 4lxl coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Wang W-C, Chu C-H, Chen C-C

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131801 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4B Chain: A
Molecule details ›
Chain: A
Length: 368 amino acids
Theoretical weight: 42.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O94953 (Residues: 1-348; Coverage: 32%)
Gene names: JHDM3B, JMJD2B, KDM4B, KIAA0876
Sequence domains:
Structure domains: Cupin
Histone H3.1 Chain: D
Molecule details ›
Chain: D
Length: 8 amino acids
Theoretical weight: 849 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 8-15; Coverage: 6%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

3 bound ligands:
Ligand PD2 1 x PD2
Ligand NI 1 x NI
Ligand ZN 1 x ZN
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL12B2
Spacegroup: P212121
Unit cell:
a: 54.364Å b: 78.475Å c: 83.893Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.222
Expression systems:
  • Escherichia coli
  • Not provided

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