4E9G Hydrolase Dna date Mar 21, 2012
title Structure Of The Glycosylase Domain Of Mbd4 Bound To Thymine Containing Dna
authors S.Morera, A.Vigouroux
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 4
Chain: A
Fragment: Glycosylase Domain Of Mbd4 (Residues 426-580)
Synonym: Methyl-Cpg-Binding Endonuclease 1, Methyl-Cpg-Bind Protein Mbd4, Mismatch-Specific Dna N-Glycosylase;
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mbd4, Med1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpcpapgpcpgptpgpcpapgpc)-3'
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna (5'-D(Gpcptpgpcpgpcpgpcptpgpg)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.080 61.470 96.560 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand
enzyme Hydrolase E.C.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceBiochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA., Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA, Nucleic Acids Res. 2012 Jul 30. PMID:22848106
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (4e9g.pdb1.gz) 35 Kb
  • CSU: Contacts of Structural Units for 4E9G
  • Structure Factors (64 Kb)
  • Retrieve 4E9G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4E9G from S2C, [Save to disk]
  • Re-refined 4e9g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4E9G 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 4E9G
  • 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 4E9G, from MSDmotif at EBI
  • Fold representative 4e9g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4e9g_A] [4e9g_C] [4e9g] [4e9g_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4E9G
  • Community annotation for 4E9G at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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