PDB entry 3vyq

View 3vyq on RCSB PDB site
Description: Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1
Class: hydrolase/DNA
Keywords: methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex
Deposited on 2012-10-02, released 2013-01-16
The last revision prior to the SCOPe 2.07 freeze date was dated 2013-08-14, with a file datestamp of 2013-08-09.
Experiment type: XRAY
Resolution: 2.52 Å
R-factor: 0.195
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Methyl-CpG-binding domain protein 4
    Species: Mus musculus [TaxId:10090]
    Gene: Mbd4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3vyqa_
  • Chain 'B':
    Compound: DNA (5'-d(*ap*cp*ap*tp*cp*(5cm)p*gp*gp*tp*gp*a)-3')
  • Chain 'C':
    Compound: DNA (5'-d(*tp*cp*ap*cp*tp*gp*gp*ap*tp*gp*t)-3')
  • Chain 'D':
    Compound: Methyl-CpG-binding domain protein 4
    Species: Mus musculus [TaxId:10090]
    Gene: Mbd4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3vyqd_
  • Heterogens: ZN, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3vyqA (A:)
    sttateghkpvpcgwervvkqrlsgktagkfdvyfispqglkfrskrslanyllkngetf
    lkpedfnftvlpkg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vyqA (A:)
    hkpvpcgwervvkqrlsgktagkfdvyfispqglkfrskrslanyllkngetflkpedfn
    ftv
    

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3vyqD (D:)
    sttateghkpvpcgwervvkqrlsgktagkfdvyfispqglkfrskrslanyllkngetf
    lkpedfnftvlpkg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vyqD (D:)
    hkpvpcgwervvkqrlsgktagkfdvyfispqglkfrskrslanyllkngetflkpedfn
    ftv