4DK9 Hydrolase Dna date Feb 03, 2012
title Crystal Structure Of Mbd4 Catalytic Domain Bound To Abasic D
authors B.A.Manvilla, E.A.Toth, A.C.Drohat
compound source
Molecule: 5'-D(Apapgpapcpgptpgpgpapc)-3'
Chain: B
Engineered: Yes
Other_details: Complementary Dna Strand
Synthetic: Yes

Molecule: 5'-D(Tpgptpcpcpap(3dr)Pgptpcpt)-3'
Chain: C
Engineered: Yes
Other_details: Abasic Dna Strand

Synthetic: Yes

Molecule: Methyl-Cpg-Binding Domain Protein 4
Chain: A
Fragment: Catalytic Domain (Unp 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
Expression_system_strain: Bl21(De3) Gold
Expression_system_vector_type: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.259
length a length b length c angle alpha angle beta angle gamma
40.999 55.161 122.193 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.76 Å
ligand 3DR, K enzyme Hydrolase E.C.3.2.2 BRENDA

Primary referenceCrystal Structure of Human Methyl-Binding Domain IV Glycosylase Bound to Abasic DNA., Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat AC, J Mol Biol. 2012 May 2. PMID:22560993
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4dk9.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 4DK9
  • CSU: Contacts of Structural Units for 4DK9
  • Structure Factors (112 Kb)
  • Retrieve 4DK9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DK9 from S2C, [Save to disk]
  • Re-refined 4dk9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DK9 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 4DK9
  • 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 4DK9, from MSDmotif at EBI
  • Fold representative 4dk9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dk9_A] [4dk9_B] [4dk9_C] [4dk9]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4DK9
  • Community annotation for 4DK9 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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