1S19 Gene Regulation date Jan 06, 2004
title Crystal Structure Of Vdr Ligand Binding Domain Complexed To Calcipotriol.
authors G.Tocchini-Valentini, N.Rochel, J.M.Wurtz, D.Moras
compound source
Molecule: Vitamin D3 Receptor
Chain: A
Fragment: Vdr Ligand Binding Domain
Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vdr, Nr1i1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 21 21 21
R_factor 0.179 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.248 52.550 132.909 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand MC9 enzyme
related structures by homologous chain: 1RJK, 1RK3
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of the vitamin D nuclear receptor liganded with the vitamin D side chain analogues calcipotriol and seocalcitol, receptor agonists of clinical importance. Insights into a structural basis for the switching of calcipotriol to a receptor antagonist by further side chain modification., Tocchini-Valentini G, Rochel N, Wurtz JM, Moras D, J Med Chem 2004 Apr 8;47(8):1956-61. PMID:15055995
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1s19.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 1S19
  • CSU: Contacts of Structural Units for 1S19
  • Likely Quarternary Molecular Structure file(s) for 1S19
  • Structure Factors (194 Kb)
  • Retrieve 1S19 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S19 from S2C, [Save to disk]
  • Re-refined 1s19 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1S19 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 1S19
  • 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 1S19, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s19a_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s19] [1s19_A]
  • SWISS-PROT database: [P11473]
  • Belongs to the vitamin d3 receptor (vdr) family according to TCDB.
  • Domain organization of [VDR_HUMAN] by SWISSPFAM
  • Domain found in 1S19: [HOLI ] by SMART
  • Other resources with information on 1S19
  • Community annotation for 1S19 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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