› 6c2f

X-ray diffraction
2.65Å resolution

MBD2 in complex with methylated DNA

Released:
DOI: 10.2210/pdb6c2f/pdb
PDB entry 6c2f coloured by chain, front view.
PDB entry 6c2f coloured by chain, side view.
PDB entry 6c2f coloured by chain, top view.
Source organisms:
Entry authors: Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C, Edwards AM, Min J, Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Function and Biology Details

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-119649 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Methyl-CpG-binding domain protein 2 Chains: A, D, G, J, M, P
Molecule details ›
Chains: A, D, G, J, M, P
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 Chains: B, E, H, K, N, Q
Molecule details ›
Chains: B, E, H, K, N, Q
Length: 12 nucleotides
Theoretical weight: 3.73 KDa
Source organism: synthetic construct
Expression system: Not provided
12-mer DNA Chains: C, F, I, L, O, R
Molecule details ›
Chains: C, F, I, L, O, R
Length: 12 nucleotides
Theoretical weight: 3.61 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 11 x UNX
1 modified residue:
Ligand 5CM 6 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P1
Unit cell:
a: 40.51Å b: 40.6Å c: 202.38Å
α: 90.07° β: 93.11° γ: 119.75°
R-values:
R R work R free
0.213 0.212 0.242
Expression systems:
  • Escherichia coli
  • Not provided

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