› 5plb

X-ray diffraction
1.49Å resolution

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 132)

Released:
DOI: 10.2210/pdb5plb/pdb
PDB entry 5plb coloured by chain, front view.
PDB entry 5plb coloured by chain, side view.
PDB entry 5plb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F
OpenAccess logo Nat Commun 8 15123 (2017)
PMID: 28436492

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-179408 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 4D Chain: A
Molecule details ›
Chain: A
Length: 364 amino acids
Theoretical weight: 42.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6B0I6 (Residues: 1-342; Coverage: 65%)
Gene names: JHDM3D, JMJD2D, KDM4D
Sequence domains:
Structure domains: Cupin

Ligands and Environments

6 bound ligands:
Ligand ZN 1 x ZN
Ligand NI 1 x NI
Ligand MG 1 x MG
Ligand OGA 1 x OGA
Ligand EDO 8 x EDO
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 71.665Å b: 71.665Å c: 150.762Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.151 0.178
Expression system: Escherichia coli

Quick links

Citations

16 review citations

WD40 repeat domain proteins: a novel target class?
Schapira et al. (2017)
15 more