PDBe 4qen

X-ray diffraction
2Å resolution

crystal structure of KRYPTONITE in complex with mCHH DNA and SAH

Released:

Function and Biology Details

Reaction catalysed:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 Chain: A
Molecule details ›
Chain: A
Length: 533 amino acids
Theoretical weight: 59.69 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8GZB6 (Residues: 93-624; Coverage: 85%)
Gene names: At5g13960, KYP, MAC12.7, SDG33, SET33, SUVH4
Sequence domains:
Structure domains: SET domain
DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*TP*CP*AP*GP*TP*AP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.59 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 54.395Å b: 98.009Å c: 122.581Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided