2D5V Transcription Dna date Nov 07, 2005
title Crystal Structure Of Hnf-6alpha Dna-Binding Domain In Comple Ttr Promoter
authors D.Iyaguchi, M.Yao, N.Watanabe, J.Nishihira, I.Tanaka
compound source
Molecule: 5'-D(Tpcptpapapgptpcpapaptpapapt)-3
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Aptptpaptptpgpapcptptpapgpa)-3
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Hepatocyte Nuclear Factor 6
Chain: A, B
Fragment: Residues 1-156
Synonym: Hnf-6, One Cut Domain Family Member 1
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1 2 1
R_factor 0.245 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.020 38.958 106.500 90.00 107.63 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ACT, GOL enzyme
note 2D5V is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6., Iyaguchi D, Yao M, Watanabe N, Nishihira J, Tanaka I, Structure. 2007 Jan;15(1):75-83. PMID:17223534
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (2d5v.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (2d5v.pdb2.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 2D5V
  • CSU: Contacts of Structural Units for 2D5V
  • Likely Quarternary Molecular Structure file(s) for 2D5V
  • Structure Factors (296 Kb)
  • Retrieve 2D5V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D5V from S2C, [Save to disk]
  • Re-refined 2d5v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D5V 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 2D5V
  • 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 2D5V, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d5v_C] [2d5v] [2d5v_D] [2d5v_B] [2d5v_F] [2d5v_A] [2d5v_E]
  • SWISS-PROT database: [P70512]
  • Domain organization of [HNF6_RAT] by SWISSPFAM
  • Domains found in 2D5V: [CUT] [HOX ] by SMART
  • Other resources with information on 2D5V
  • Community annotation for 2D5V 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science