› 4do0

X-ray diffraction
2.55Å resolution

Crystal Structure of human PHF8 in complex with Daminozide

Released:
DOI: 10.2210/pdb4do0/pdb
PDB entry 4do0 coloured by chain, front view.
PDB entry 4do0 coloured by chain, side view.
PDB entry 4do0 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Krojer T, Daniel M, Ng SS, Walport LJ, Chowdhury R, Arrowsmith CH, Edwards A, Bountra C, Kawamura A, Muller-Knapp S, McDonough MA, von Delft F, Schofield CJ, Oppermann U, Structural Genomics Consortium (SGC)

Function and Biology Details

Reactions catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(36) + succinate + formaldehyde + CO(2)
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194030 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone lysine demethylase PHF8 Chain: A
Molecule details ›
Chain: A
Length: 374 amino acids
Theoretical weight: 43.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UPP1 (Residues: 115-483; Coverage: 35%)
Gene names: KIAA1111, PHF8, ZNF422
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand DZA 1 x DZA
Ligand ZN 1 x ZN
Ligand SO4 6 x SO4
Ligand EDO 3 x EDO
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: I213
Unit cell:
a: 151.734Å b: 151.734Å c: 151.734Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.208 0.265
Expression system: Escherichia coli

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