› 2ma5

Solution NMR

Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C

Released:
DOI: 10.2210/pdb2ma5/pdb
PDB entry 2ma5 coloured by chain, ensemble of 20 models, front view.
PDB entry 2ma5 coloured by chain, ensemble of 20 models, side view.
PDB entry 2ma5 coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Entry authors: Hassan F, Ramelot TA, Yang Y, Cort JR, Janjua H, Kohan E, Lee D, Xiao R, Acton TB, Everett JK, Montelione GT, Kennedy MA, Northeast Structural Genomics Consortium (NESG)

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:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5B Chain: A
Molecule details ›
Chain: A
Length: 61 amino acids
Theoretical weight: 6.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UGL1 (Residues: 1487-1544; Coverage: 4%)
Gene names: JARID1B, KDM5B, PLU1, RBBP2H1
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
Chemical shift assignment: 95%
Refinement method: simulated annealing, null
Expression system: Escherichia coli BL21(DE3)

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