› 2e6r

Solution NMR

Solution structure of the PHD domain in SmcY protein

Released:
DOI: 10.2210/pdb2e6r/pdb
PDB entry 2e6r coloured by chain, ensemble of 20 models, front view.
PDB entry 2e6r coloured by chain, ensemble of 20 models, side view.
PDB entry 2e6r coloured by chain, ensemble of 20 models, top view.
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
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
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:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

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

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