2VI6 Transcription date Nov 28, 2007
title Crystal Structure Of The Nanog Homeodomain
authors R.Jauch, C.K.L.Ng, K.S.Saitakendu, R.C.Stevens, P.R.Kolatkar
compound source
Molecule: Homeobox Protein Nanog
Chain: A, B, C, D, E, F, G, H
Fragment: Homeodomain, Residues 96-155
Synonym: Homeobox Transcription Factor Nanog, Early Embryo Expression Nk-Type Homeobox Protein, Es Cell- Associated Pr Nanog;
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Petg60a
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.318 114.771 62.771 90.00 98.68 90.00
method X-Ray Diffractionresolution 2.60 Å
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceCrystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog., Jauch R, Ng CK, Saikatendu KS, Stevens RC, Kolatkar PR, J Mol Biol. 2007 Dec 4;. PMID:18177668
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (2vi6.pdb1.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb2.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb3.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb4.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb5.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb6.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb7.gz) 11 Kb
  • Biological Unit Coordinates (2vi6.pdb8.gz) 11 Kb
  • CSU: Contacts of Structural Units for 2VI6
  • Likely Quarternary Molecular Structure file(s) for 2VI6
  • Structure Factors (167 Kb)
  • Retrieve 2VI6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VI6 from S2C, [Save to disk]
  • Re-refined 2vi6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VI6 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 2VI6
  • 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
  • 3D motif for 2VI6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vi6] [2vi6_D] [2vi6_F] [2vi6_E] [2vi6_B] [2vi6_C] [2vi6_G] [2vi6_H] [2vi6_A]
  • SWISS-PROT database: [Q80Z64]
  • Domain organization of [NANOG_MOUSE] by SWISSPFAM
  • Domain found in 2VI6: [HOX ] by SMART
    • Other resources with information on 2VI6
  • Community annotation for 2VI6 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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