5KE6 Transcription Dna date Jun 09, 2016
title Mouse Klf4 Znf1-3 And Tpgcpa Sequence Dna Complex Structure
authors H.Hashimoto, X.Cheng
compound source
Molecule: Krueppel-Like Factor 4
Chain: A
Fragment: Unp Residues 396-483
Synonym: Epithelial Zinc Finger Protein Ezf,Gut-Enriched Kr Like Factor;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Klf4, Ezf, Gklf, Zie
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Codon Plus
Expression_system_vector_type: Pgex-6p-1
Expression_system_plasmid: Pxc1248

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.198 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.870 50.870 130.540 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.99 Å
ligand ZN enzyme
Primary referenceDistinctive Klf4 mutants determine preference for DNA methylation status., Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X, Nucleic Acids Res. 2016 Sep 4. pii: gkw774. PMID:27596594
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (5ke6.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 5KE6
  • CSU: Contacts of Structural Units for 5KE6
  • Structure Factors (252 Kb)
  • Retrieve 5KE6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KE6 from S2C, [Save to disk]
  • Re-refined 5ke6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KE6 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 5KE6
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ke6] [5ke6_A] [5ke6_B] [5ke6_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5KE6: [ZnF_C2H2 ] by SMART
  • Other resources with information on 5KE6
  • Community annotation for 5KE6 at PDBWiki (http://pdbwiki.org)

  • 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science