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Yorodumi- PDB-3vyq: Crystal structure of the methyl CpG Binding Domain of MBD4 in com... -
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-Basic information
Entry | Database: PDB / ID: 3vyq | ||||||
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Title | Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1 | ||||||
Components |
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Keywords | HYDROLASE/DNA / methyl CpG binding domain / protein-DNA complex / versatile base recognition / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin ...Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.525 Å | ||||||
Authors | Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Ariyoshi, M. / Shirakawa, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4 Authors: Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Kimura, H. / Suetake, I. / Tajima, S. / Ariyoshi, M. / Shirakawa, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vyq.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vyq.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vyq_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 3vyq_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 3vyq_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 3vyq_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vyq ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vyq | HTTPS FTP |
-Related structure data
Related structure data | 3vxvSC 3vxxC 3vybC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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