› 5rb3

X-ray diffraction
1.53Å resolution

PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS039249d

Released:
DOI: 10.2210/pdb5rb3/pdb
PDB entry 5rb3 coloured by chain, front view.
PDB entry 5rb3 coloured by chain, side view.
PDB entry 5rb3 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Snee M, Nowak R, Johansson C, Burgess-Brown NA, Arrowsmith CH, Bountra C, Edwards AM, 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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 372 amino acids
Theoretical weight: 43.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7LBC6 (Residues: 1380-1728; Coverage: 20%)
Gene names: C5orf7, JHDM2B, JMJD1B, KDM3B, KIAA1082
Sequence domains: JmjC domain, hydroxylase

Ligands and Environments

3 bound ligands:
Ligand MPV 3 x MPV
Ligand CL 5 x CL
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 58.04Å b: 93.46Å c: 94.34Å
α: 90° β: 107.86° γ: 90°
R-values:
R R work R free
0.188 0.187 0.208
Expression system: Escherichia coli

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