› 4lg7

X-ray diffraction
2.5Å resolution

Crystal structure MBD4 MBD domain in complex with methylated CpG DNA

Released:
DOI: 10.2210/pdb4lg7/pdb
PDB entry 4lg7 coloured by chain, front view.
PDB entry 4lg7 coloured by chain, side view.
PDB entry 4lg7 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Xu C, Tempel W, Wernimont AK, Bountra C, Arrowsmith CH, Edwards AM, Min J, 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-117788 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methyl-CpG-binding domain protein 4 Chain: A
Molecule details ›
Chain: A
Length: 68 amino acids
Theoretical weight: 7.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95243 (Residues: 83-149; Coverage: 12%)
Gene names: MBD4, MED1
Sequence domains: Methyl-CpG binding domain
Structure domains: Methyl-cpg-binding Protein 2; Chain A
DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3') Chains: B, C
Molecule details ›
Chains: B, C
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 11 x UNX
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P21212
Unit cell:
a: 49.367Å b: 78.209Å c: 40.557Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.212 0.259
Expression systems:
  • Escherichia coli
  • Not provided

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