› 5phg

X-ray diffraction
1.4Å resolution

PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09689a

Released:
DOI: 10.2210/pdb5phg/pdb
PDB entry 5phg coloured by chain, front view.
PDB entry 5phg coloured by chain, side view.
PDB entry 5phg 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 OGA 1 x OGA
Ligand EDO 8 x EDO
Ligand SO4 4 x SO4
Ligand 8P4 1 x 8P4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 71.567Å b: 71.567Å c: 150.561Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.13 0.168
Expression system: Escherichia coli

Quick links

Citations

16 review citations

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

1 mention without citation

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.
Pearce et al. (2017)