3D5F Transcription date May 16, 2008
title Crystal Structure Of Ppar-Delta Complex
authors Y.Amano
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Delta
Chain: A, B
Fragment: Ligand Binding Domain, Unp Residues 175-441
Synonym: Ppar-Delta, Ppar-Beta, Nuclear Receptor Subfamily Member 2, Nuclear Hormone Receptor 1, Nuc1, Nuci;
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: P 1 21 1
R_factor 0.278 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.456 92.829 96.454 90.00 98.02 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand L41 BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (3d5f.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (3d5f.pdb2.gz) 44 Kb
  • Biological Unit Coordinates (3d5f.pdb3.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3D5F
  • CSU: Contacts of Structural Units for 3D5F
  • Likely Quarternary Molecular Structure file(s) for 3D5F
  • Structure Factors (254 Kb)
  • Retrieve 3D5F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D5F from S2C, [Save to disk]
  • Re-refined 3d5f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3D5F 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 3D5F
  • 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 3D5F, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d5f_A] [3d5f] [3d5f_B]
  • SWISS-PROT database: [Q03181]
  • Domain organization of [PPARD_HUMAN] by SWISSPFAM
  • Domain found in 3D5F: [HOLI ] by SMART
    • Other resources with information on 3D5F
  • Community annotation for 3D5F 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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