› 2yyr

X-ray diffraction
2.5Å resolution

Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide

Released:
DOI: 10.2210/pdb2yyr/pdb
PDB entry 2yyr coloured by chain, front view.
PDB entry 2yyr coloured by chain, side view.
PDB entry 2yyr coloured by chain, top view.
Source organism: Mus musculus
Entry authors: Nakamura Y, Padmanabhan B, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163373 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pygopus homolog 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 67 amino acids
Theoretical weight: 7.33 KDa
Source organism: Mus musculus
Expression system: cell-free protein synthesis
UniProt:
  • Canonical: Q9D0P5 (Residues: 330-396; Coverage: 16%)
Gene name: Pygo1
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
H3K4Me3 peptide Chain: P
Molecule details ›
Chain: P
Length: 8 amino acids
Theoretical weight: 976 Da
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
2 modified residues:
Ligand MSE 4 x MSE
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P43212
Unit cell:
a: 59.518Å b: 59.518Å c: 95.853Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.213 0.234
Expression system: Not provided

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