6c1t

X-ray diffraction
1.84Å resolution

MBD2 in complex with a partially methylated DNA

Released:

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-119645 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Methyl-CpG-binding domain protein 2 Chains: A, D
Molecule details ›
Chains: A, D
Length: 79 amino acids
Theoretical weight: 8.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBB5 (Residues: 143-220; Coverage: 19%)
Gene name: MBD2
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
12-mer DNA Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.6 KDa
Source organism: synthetic construct
Expression system: Not provided
12-mer DNA Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2
Unit cell:
a: 71.473Å b: 36.933Å c: 104.076Å
α: 90° β: 108.25° γ: 90°
R-values:
R R work R free
0.215 0.214 0.247
Expression systems:
  • Escherichia coli
  • Not provided