POP-OUT | CLOSE
Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1
DOI:10.2210/pdb3vyq/pdb   NDB ID: NA2058
3VYQ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/dna
    Structure Weight: 23660.07
    Molecule: Methyl-CpG-binding domain protein 4
    Polymer: 1 Type: protein Length: 74
    Chains: A, D
    EC#: 3.2.2   
    Fragment: methyl CpG binding domain, UNP residues 63-136
    Organism Mus musculus
    Gene Name Mbd4
    UniProtKB:   Protein Feature View | Search PDB | Q9Z2D7  
    Molecule: DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3')
    Polymer: 2 Type: dna Length: 11
    Chains: B
    Molecule: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3')
    Polymer: 3 Type: dna Length: 11
    Chains: C
     
  •   Structure Validation Hide

    Download full validation report    

     
  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Mus musculus   Taxonomy   Common Name: Mouse Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3VXV   
    3VXX   
    3VYB   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    EDO
    Search 
    Download 
    EDO C2 H6 O2
    1,2-ETHANEDIOL
    ZN
    Search 
    Download 
    ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    5CM
    Search 
    5CM C10 H16 N3 O7 P DC dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2058
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
Downloadable viewers:
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Otani, J.,  Arita, K.,  Kato, T.,  Kinoshita, M.,  Ariyoshi, M.,  Shirakawa, M.

    Deposition:   2012-10-02
    Release:   2013-01-16
    Last Modified (REVDAT):   2013-08-14
     
  •   Revision History    Hide
    Mouse over text for details
    2013-08-14
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.53
    R-Value: 0.195 (obs.)
    R-Free: 0.236
    Space Group: P 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 30.60 α = 75.28 
    b = 34.09 β = 77.76 
    c = 61.17 γ = 87.31