› 6x9j

X-ray diffraction
1.79Å resolution

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
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-511276 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 1 Chain: A
Molecule details ›
Chain: A
Length: 874 amino acids
Theoretical weight: 98.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P26358 (Residues: 729-1600; Coverage: 54%)
Gene names: AIM, CXXC9, DNMT, DNMT1
Sequence domains:
DNA (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*AP*GP*G)-R(P*(PYO))-D(P*GP*GP*CP*CP*TP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.67 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand EDO 17 x EDO
Ligand X52 1 x X52
2 modified residues:
Ligand 5CM 1 x 5CM
Ligand PYO 1 x PYO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 160.058Å b: 77.765Å c: 116.72Å
α: 90° β: 125.353° γ: 90°
R-values:
R R work R free
0.201 0.2 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

21 review citations

An Epigenetic Role of Mitochondria in Cancer.
Liu et al. (2022)
20 more

3 mentions without citation

Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia.
Pappalardi et al. (2021)
2 more