5vah

X-ray diffraction
2.4Å resolution

Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26

Released:

Function and Biology Details

Reaction catalysed:
S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-110882 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Probable Histone-lysine N-methyltransferase ATXR5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 229 amino acids
Theoretical weight: 26.22 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli
UniProt:
  • Canonical: B9RU15 (Residues: 146-374; Coverage: 61%)
Gene names: ATXR5, RCOM_1460410
Sequence domains: SET domain
Structure domains: SET domain
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 15 amino acids
Theoretical weight: 1.42 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
UniProt:
  • Canonical: P59226 (Residues: 22-36; Coverage: 11%)
Gene names: At1g09200, At3g27360, At5g10390, At5g10400, At5g65360, F12B17_250, F12B17_260, HTR1, HTR13, HTR2, HTR3, HTR9, K1G2.8, MNA5.9, T12M4.9

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: C2
Unit cell:
a: 101.201Å b: 87.188Å c: 74.022Å
α: 90° β: 127.87° γ: 90°
R-values:
R R work R free
0.23 0.228 0.281
Expression systems:
  • Escherichia coli
  • Not provided