› 3swr

X-ray diffraction
2.49Å resolution

Structure of human DNMT1 (601-1600) in complex with Sinefungin

Released:
DOI: 10.2210/pdb3swr/pdb
PDB entry 3swr coloured by chain, front view.
PDB entry 3swr coloured by chain, side view.
PDB entry 3swr coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Hashimoto H, Cheng X

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150711 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 1 Chain: A
Molecule details ›
Chain: A
Length: 1002 amino acids
Theoretical weight: 113.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P26358 (Residues: 601-1600; Coverage: 62%)
Gene names: AIM, CXXC9, DNMT, DNMT1
Sequence domains:

Ligands and Environments


Cofactor: Ligand SFG 1 x SFG
4 bound ligands:
Ligand SO4 1 x SO4
Ligand MES 2 x MES
Ligand EDO 25 x EDO
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 60Å b: 110.77Å c: 201.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.272
Expression system: Escherichia coli

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