› 5chz

X-ray diffraction
1.83Å resolution

Structure of wild-type human MBD4 bound to a G:T mismatch

Released:
DOI: 10.2210/pdb5chz/pdb
PDB entry 5chz coloured by chain, front view.
PDB entry 5chz coloured by chain, side view.
PDB entry 5chz coloured by chain, top view.
Source organisms:
Entry authors: Ouzon-Shubeita H, Lin Y-L, Lee S

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118481 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Methyl-CpG-binding domain protein 4 Chain: A
Molecule details ›
Chain: A
Length: 192 amino acids
Theoretical weight: 22.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O95243 (Residues: 426-580; Coverage: 27%)
Gene names: MBD4, MED1
Structure domains: Hypothetical protein; domain 2
7-mer DNA Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.1 KDa
Source organism: synthetic construct
Expression system: Not provided
12-mer DNA(G) Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: synthetic construct
Expression system: Not provided
5-mer DNA Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.51 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P212121
Unit cell:
a: 41.886Å b: 54.875Å c: 104.522Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.174 0.209
Expression systems:
  • Escherichia coli BL21
  • Not provided

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