5K13 Transcription date May 17, 2016
title Crystal Structure Of The Rar Alpha Ligand-Binding Domain In With An Antagonist
authors Y.Wang, S.L.Stout
compound source
Molecule: Retinoic Acid Receptor Alpha
Chain: A
Fragment: Unp Residues 176-421
Synonym: Rar-Alpha,Nuclear Receptor Subfamily 1 Group B Mem
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rara, Nr1b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.195 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.496 62.541 49.347 90.00 106.05 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand 6Q7 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIdentification of potent and selective retinoic acid receptor gamma (RARgamma) antagonists for the treatment of osteoarthritis pain using structure based drug design., Hughes NE, Bleisch TJ, Jones SA, Richardson TI, Doti RA, Wang Y, Stout SL, Durst GL, Chambers MG, Oskins JL, Lin C, Adams LA, Page TJ, Barr RJ, Zink RW, Osborne H, Montrose-Rafizadeh C, Norman BH, Bioorg Med Chem Lett. 2016 Jul 15;26(14):3274-7. doi: 10.1016/j.bmcl.2016.05.056., Epub 2016 May 20. PMID:27261179
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (5k13.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 5K13
  • CSU: Contacts of Structural Units for 5K13
  • Structure Factors (1485 Kb)
  • Retrieve 5K13 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K13 from S2C, [Save to disk]
  • Re-refined 5k13 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K13 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 5K13
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k13_A] [5k13]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5K13: [HOLI ] by SMART
  • Other resources with information on 5K13
  • Community annotation for 5K13 at PDBWiki (http://pdbwiki.org)

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