3WWR Transcription date Jun 27, 2014
title Crystal Structure Of The Human Vitamin D Receptor Ligand Bin Domain Complexed With 1-((((1s,2r,6r,Z)-2,6-Dihydroxy-4-((E 3as,7ar)-1-((R)-6-Hydroxy-6-Methylheptan-2-Yl)-7a-Methylhex Inden-4(2h)-Ylidene)Ethylidene)-3-Methylenecyclohexyl)Oxy)M Cyclopropanecarbonitrile
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
symmetry Space Group: P 21 21 21
R_factor 0.247 R_Free 0.291
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.167 51.826 132.384 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.18 Å
ligand 3AJ enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSynthesis and biological activities of vitamin D derivatives with cyanoalkyl side chain at C-2 position., Saitoh H, Watanabe H, Kakuda S, Takimoto-Kamimura M, Takagi K, Takeuchi A, Takenouchi K, J Steroid Biochem Mol Biol. 2014 Dec 10. pii: S0960-0760(14)00310-0. doi:, 10.1016/j.jsbmb.2014.12.004. PMID:25500068
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (3wwr.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 3WWR
  • CSU: Contacts of Structural Units for 3WWR
  • Structure Factors (106 Kb)
  • Retrieve 3WWR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WWR from S2C, [Save to disk]
  • Re-refined 3wwr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WWR 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 3WWR
  • 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 3WWR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wwr] [3wwr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3WWR: [HOLI ] by SMART
  • Other resources with information on 3WWR
  • Community annotation for 3WWR at PDBWiki (http://pdbwiki.org)

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