2e6r

Solution NMR

Solution structure of the PHD domain in SmcY protein

Released:
Source organism: Homo sapiens
Entry authors: Kadirvel S, He F, Muto Y, Inoue M, Kigawa T, Shirouzu M, Terada T, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-189820 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5D Chain: A
Molecule details ›
Chain: A
Length: 92 amino acids
Theoretical weight: 10.02 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9BY66 (Residues: 306-384; Coverage: 5%)
Gene names: HY, HYA, JARID1D, KDM5D, KIAA0234, SMCY
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: torsion angle dynamics
Expression system: Not provided