4E9F Hydrolase Dna date Mar 21, 2012
title Structure Of The Glycosylase Domain Of Mbd4 Bound To Ap Site 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
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(Cpcpapgpcpgp(3dr)Pgpcpapgpc
Chain: C
Engineered: Yes
Other_details: Dna Fragment With 3dr Site

Synthetic: Yes
Other_details: Synthetic Dna

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

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
41.070 55.840 96.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand 3DR, EDO enzyme Hydrolase E.C.3.2.2 BRENDA

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] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (4e9f.pdb1.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 4E9F
  • CSU: Contacts of Structural Units for 4E9F
  • Structure Factors (123 Kb)
  • Retrieve 4E9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4E9F from S2C, [Save to disk]
  • Re-refined 4e9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4E9F in 3D
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  • 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 4E9F, from MSDmotif at EBI
  • Fold representative 4e9f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4e9f_A] [4e9f] [4e9f_D] [4e9f_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4E9F
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