3VXV Hydrolase Dna date Sep 21, 2012
title Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4 In Co The 5mcgtg Sequence
authors J.Otani, K.Arita, T.Kato, M.Kinoshita, M.Ariyoshi, M.Shirakawa
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 4
Chain: A
Fragment: Methyl Cpg Binding Domain, Unp Residues 69-136
Synonym: Methyl-Cpg-Binding Protein Mbd4, Mismatch-Specific Glycosylase;
Ec: 3.2.2.-
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Mbd4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Dna (5'-D(Gptpcpapcptpapcp(5cm)Pgpgpa 3');
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Gptpcptpgpgptpapgptpgpapcp
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.188 R_Free 0.224
length a length b length c angle alpha angle beta angle gamma
89.074 94.989 54.738 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 5CM, ACT, EDO enzyme Hydrolase E.C.3.2.2 BRENDA

Primary referenceStructural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4., Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M, J Biol Chem. 2013 Mar 1;288(9):6351-62. doi: 10.1074/jbc.M112.431098. Epub 2013, Jan 10. PMID:23316048
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (3vxv.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 3VXV
  • CSU: Contacts of Structural Units for 3VXV
  • Structure Factors (176 Kb)
  • Retrieve 3VXV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VXV from S2C, [Save to disk]
  • Re-refined 3vxv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VXV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3VXV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3VXV, from MSDmotif at EBI
  • Fold representative 3vxv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vxv_B] [3vxv] [3vxv_A] [3vxv_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VXV: [MBD ] by SMART
  • Other resources with information on 3VXV
  • Community annotation for 3VXV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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