5GT4 Transcription date Aug 18, 2016
title Crystal Structure Of The Human Vitamin D Receptor Ligand Bin Domain Complexed With (1r,2s,3r,5z,7e,14beta,17alpha)-2-Cya 9,10-Secocholesta-5,7,10-Triene-1,3,25-Triol
authors M.Takimoto-Kamimura
compound source
Molecule: Vitamin D3 Receptor
Chain: A
Fragment: Unp Residues 118-164,216-423
Synonym: Vdr,1,25-Dihydroxyvitamin D3 Receptor,Nuclear Rece Subfamily 1 Group I Member 1;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vdr, Nr1i1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.663 51.842 131.475 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.83 Å
ligand 2KB enzyme
note 5GT4 supersedes 4PA2
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (5gt4.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 5GT4
  • CSU: Contacts of Structural Units for 5GT4
  • Structure Factors (1852 Kb)
  • Retrieve 5GT4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GT4 from S2C, [Save to disk]
  • Re-refined 5gt4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5GT4 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 5GT4
  • 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: [5gt4] [5gt4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5GT4: [HOLI ] by SMART
    • Other resources with information on 5GT4
  • Community annotation for 5GT4 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