3VYQ	Hydrolase Dna	date	Oct 02, 2012
title	Crystal Structure Of The Methyl Cpg Binding Domain Of Mbd4 I With The 5mcgtg Sequence In Space Group P1
authors	J.Otani, K.Arita, T.Kato, M.Kinoshita, M.Ariyoshi, M.Shirakawa
compound		source
Molecule: Methyl-Cpg-Binding Domain Protein 4 Chain: A, D Fragment: Methyl Cpg Binding Domain, Unp Residues 63-136 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(Apcpaptpcp(5cm)Pgpgptpgpa)-3 Chain: B Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Tpcpapcptpgpgpaptpgpt)-3') Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1	R_factor 0.193 R_Free 0.237
crystal cell	length a length b length c angle alpha angle beta angle gamma 30.604 34.093 61.165 75.28 77.76 87.31
method	X-Ray Diffraction	resolution	2.53 Å
ligand	5CM, EDO, ZN	enzyme	Hydrolase E.C.3.2.2 BRENDA
Gene Ontology	Chain Function Process Component A, D
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] (65 Kb) [Save to disk] Biological Unit Coordinates (3vyq.pdb1.gz) 60 Kb LPC: Ligand-Protein Contacts for 3VYQ CSU: Contacts of Structural Units for 3VYQ Structure Factors (108 Kb) Retrieve 3VYQ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3VYQ from S2C, [Save to disk] Re-refined 3vyq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3VYQ 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 3VYQ

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3VYQ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3vyq_D] [3vyq] [3vyq_B] [3vyq_C] [3vyq_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3VYQ: [MBD ] by SMART

Other resources with information on 3VYQ

Community annotation for 3VYQ at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---