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
crystal cell	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 Diffraction	resolution	2.00 Å
ligand	5CM, ACT, EDO	enzyme	Hydrolase E.C.3.2.2 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structural 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

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 3D motif for 3VXV, from MSDmotif at EBI

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)

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