3QMI Dna Binding Protein Dna date Feb 04, 2011
title Structural Basis Of Selective Binding Of Non-Methylated Cpg (Dna-Acgt) By The Cxxc Domain Of Cfp1
authors C.Xu, C.Bian, F.Mackenzie, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc)
compound source
Molecule: Cpg-Binding Protein
Chain: A
Fragment: Cxxc-Type Zn Finger, Residues 161-222
Synonym: Cxxc-Type Zinc Finger Protein 1, Phd Finger And Cx Containing Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cfp1, Cgbp, Cxxc1, Pccx1, Phf18
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Bl21-V2r-Prare2

Molecule: 5'-D(Gpcpcpapapcpgptptpgpgpc)-3'
Chain: B, C
Fragment: Dna (Nonmethylated Cpg Island)
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.207 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
30.624 75.009 125.905 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand PEG, PO4, ZN enzyme

Primary referenceThe structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain., Xu C, Bian C, Lam R, Dong A, Min J, Nat Commun. 2011 Mar;2:227. PMID:21407193
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (25 Kb) [Save to disk]
  • Biological Unit Coordinates (3qmi.pdb1.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 3QMI
  • CSU: Contacts of Structural Units for 3QMI
  • Structure Factors (130 Kb)
  • Retrieve 3QMI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QMI from S2C, [Save to disk]
  • Re-refined 3qmi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QMI 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 3QMI
  • 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 3QMI, from MSDmotif at EBI
  • Fold representative 3qmi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qmi_A] [3qmi] [3qmi_B] [3qmi_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3QMI
  • Community annotation for 3QMI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • 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
    Bioinformatics Unit
    Weizmann Institute of Science