› 2yqe

Solution NMR

Solution structure of the ARID domain of JARID1D protein

Released:
DOI: 10.2210/pdb2yqe/pdb
PDB entry 2yqe coloured by chain, ensemble of 20 models, front view.
PDB entry 2yqe coloured by chain, ensemble of 20 models, side view.
PDB entry 2yqe coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Entry authors: Tanabe W, Suzuki S, Muto Y, Inoue M, Kigawa T, Terada T, Shirouzu M, 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:
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: 100 amino acids
Theoretical weight: 11.47 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9BY66 (Residues: 79-171; Coverage: 6%)
Gene names: HY, HYA, JARID1D, KDM5D, KIAA0234, SMCY
Sequence domains: ARID/BRIGHT DNA binding domain
Structure domains: ARID DNA-binding domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

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

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