3IHO Hydrolase date Jul 30, 2009
title The C-Terminal Glycosylase Domain Of Human Mbd4
authors M.F.Amaya, C.Xu, C.B.Bian, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, Structural Genomics Consortiu
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 4
Chain: A
Fragment: C-Terminal Glycosylase Domain
Synonym: Methyl-Cpg-Binding Protein Mbd4, Methyl-Cpg-Bindin Endonuclease 1, 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
symmetry Space Group: H 3
R_factor 0.182 R_Free 0.290
length a length b length c angle alpha angle beta angle gamma
83.541 83.541 73.956 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
enzyme Hydrolase E.C.3.2.2 BRENDA
note 3IHO is a representative structure

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (3iho.pdb1.gz) 24 Kb
  • CSU: Contacts of Structural Units for 3IHO
  • Structure Factors (37 Kb)
  • Retrieve 3IHO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IHO from S2C, [Save to disk]
  • Re-refined 3iho structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IHO 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 3IHO
  • 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 3IHO, from MSDmotif at EBI
  • Fold representative 3iho from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iho] [3iho_A]
  • SWISS-PROT database: [O95243]
  • Domain organization of [MBD4_HUMAN] by SWISSPFAM
  • Other resources with information on 3IHO
  • Community annotation for 3IHO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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