5AVI Transcription date Jun 16, 2015
title Crystal Structure Of Lxralpha In Complex With Tert-Butyl Ben Analog, Compound 4
authors Y.Matsui, H.Hanzawa, K.Tamaki
compound source
Molecule: Oxysterols Receptor Lxr-Alpha
Chain: A, C
Fragment: Ligand Binding Domain, Unp Residues 182-447
Synonym: Liver X Receptor Alpha,Nuclear Receptor Subfamily Member 3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1h3, Lxra
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Nuclear Receptor Coactivator 1
Chain: B, D
Fragment: Unp Residues 676-700
Synonym: Ncoa-1,Class E Basic Helix-Loop-Helix Protein 74,B Protein Hin-2,Rip160,Renal Carcinoma Antigen Ny-Ren-52,Ster Receptor Coactivator 1,Src-1;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 4 21 2
R_factor 0.244 R_Free 0.274
length a length b length c angle alpha angle beta angle gamma
124.356 124.356 91.916 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 4KM enzyme Transferase E.C. BRENDA
Primary referenceDiscovery and structure-guided optimization of tert-butyl 6-(phenoxymethyl)-3-(trifluoromethyl)benzoates as liver X receptor agonists., Matsui Y, Yamaguchi T, Yamazaki T, Yoshida M, Arai M, Terasaka N, Honzumi S, Wakabayashi K, Hayashi S, Nakai D, Hanzawa H, Tamaki K, Bioorg Med Chem Lett. 2015 Sep 15;25(18):3914-20. doi:, 10.1016/j.bmcl.2015.07.047. Epub 2015 Jul 23. PMID:26238323
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (175 Kb) [Save to disk]
  • Biological Unit Coordinates (5avi.pdb1.gz) 168 Kb
  • LPC: Ligand-Protein Contacts for 5AVI
  • CSU: Contacts of Structural Units for 5AVI
  • Structure Factors (374 Kb)
  • Retrieve 5AVI in mmCIF format [Save to disk]
  • Re-refined 5avi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5AVI 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 5AVI
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5avi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5avi_A] [5avi] [5avi_C] [5avi_D] [5avi_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5AVI: [HOLI ] by SMART
  • Other resources with information on 5AVI
  • Community annotation for 5AVI at PDBWiki (http://pdbwiki.org)

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