3DY6 Transcription date Jul 25, 2008
title Ppardelta Complexed With An Anthranilic Acid Partial Agonist
authors M.L.Lambert, R.Xu, B.G.Shearer, T.M.Wilson
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Delta
Chain: A, B
Fragment: Ligand Binding Domain Residues 171-441
Synonym: Ppar-Delta, Ppar- Beta, Nuclear Receptor Subfamily Member 2, Nuclear Hormone Receptor 1, Nuc1, Nuci;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Ppard, Nr1c2, Pparb
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prseta
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.886 94.324 97.066 90.00 98.30 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand DY6, IOD BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiscovery of a novel class of PPARdelta partial agonists., Shearer BG, Patel HS, Billin AN, Way JM, Winegar DA, Lambert MH, Xu RX, Leesnitzer LM, Merrihew RV, Huet S, Willson TM, Bioorg Med Chem Lett. 2008 Sep 15;18(18):5018-22. Epub 2008 Aug 9. PMID:18722772
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (3dy6.pdb1.gz) 81 Kb
  • Biological Unit Coordinates (3dy6.pdb2.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 3DY6
  • CSU: Contacts of Structural Units for 3DY6
  • Likely Quarternary Molecular Structure file(s) for 3DY6
  • Structure Factors (235 Kb)
  • Retrieve 3DY6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DY6 from S2C, [Save to disk]
  • Re-refined 3dy6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DY6 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 3DY6
  • 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 3DY6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dy6_A] [3dy6_B] [3dy6]
  • SWISS-PROT database: [Q03181]
  • Domain organization of [PPARD_HUMAN] by SWISSPFAM
  • Domain found in 3DY6: [HOLI ] by SMART
  • Other resources with information on 3DY6
  • Community annotation for 3DY6 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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