› 6d1t

X-ray diffraction
2.25Å resolution

Complex of MBD1-MBD and methylated DNA

Released:
DOI: 10.2210/pdb6d1t/pdb
PDB entry 6d1t coloured by chain, front view.
PDB entry 6d1t coloured by chain, side view.
PDB entry 6d1t 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 (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-119716 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methyl-CpG-binding domain protein 1 Chain: A
Molecule details ›
Chain: A
Length: 79 amino acids
Theoretical weight: 8.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UIS9 (Residues: 1-77; Coverage: 13%)
Gene names: CXXC3, MBD1, PCM1
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: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 12 x UNX
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 28.574Å b: 74.193Å c: 138.872Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.235 0.269
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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