PDBe 3pta

X-ray diffraction
3.6Å resolution

Crystal structure of human DNMT1(646-1600) in complex with DNA

Released:

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

Structure analysis Details

Assembly composition:
hetero trimer (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: 956 amino acids
Theoretical weight: 108.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P26358 (Residues: 646-1600; Coverage: 59%)
Gene names: AIM, CXXC9, DNMT, DNMT1
Sequence domains:
Structure domains:
DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 19 nucleotides
Theoretical weight: 5.78 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.87 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 162.8Å b: 87.9Å c: 113.9Å
α: 90° β: 97.2° γ: 90°
R-values:
R R work R free
0.257 0.257 0.291
Expression systems:
  • Escherichia coli
  • Not provided