3A2I Hormone Receptor, Transcription date May 20, 2009
title Crystal Structure Of The Human Vitamin D Receptor (H305f) Li Binding Domain Complexed With Tei-9647
authors S.Kakuda, M.Takimoto-Kamimura
compound source
Molecule: Vitamin D3 Receptor
Chain: A
Fragment: Ligand Binding Domain, Residues 118-427
Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor, Nuclear Re Subfamily 1 Group I Member 1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vdr, Nr1i1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 21 21 21
R_factor 0.218 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.796 51.365 131.773 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.27 Å
ligand TEJ enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone., Kakuda S, Ishizuka S, Eguchi H, Mizwicki MT, Norman AW, Takimoto-Kamimura M, Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):918-26. Epub 2010, Jul 10. PMID:20693691
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (3a2i.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 3A2I
  • CSU: Contacts of Structural Units for 3A2I
  • Structure Factors (77 Kb)
  • Retrieve 3A2I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A2I from S2C, [Save to disk]
  • Re-refined 3a2i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A2I 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 3A2I
  • 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 3A2I, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a2i_A] [3a2i]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3A2I: [HOLI ] by SMART
  • Other resources with information on 3A2I
  • Community annotation for 3A2I 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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