2I4J Transcription date Aug 22, 2006
title Crystal Structure Of The Complex Between Ppargamma And The A Lt160 (Ureidofibrate Derivative)
authors G.Pochetti, F.Mazza
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: A, B
Fragment: Ligand Binding Domain (Lbd), Residues 223-504
Synonym: Ppar-Gamma
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: C 1 2 1
R_factor 0.247 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.142 60.947 118.106 90.00 103.26 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand DRJ BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceInsights into the mechanism of partial agonism: crystal structures of the peroxisome proliferator-activated receptor gamma ligand-binding domain in the complex with two enantiomeric ligands., Pochetti G, Godio C, Mitro N, Caruso D, Galmozzi A, Scurati S, Loiodice F, Fracchiolla G, Tortorella P, Laghezza A, Lavecchia A, Novellino E, Mazza F, Crestani M, J Biol Chem. 2007 Apr 2;. PMID:17403688
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (2i4j.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 2I4J
  • CSU: Contacts of Structural Units for 2I4J
  • Likely Quarternary Molecular Structure file(s) for 2I4J
  • Structure Factors (266 Kb)
  • Retrieve 2I4J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I4J from S2C, [Save to disk]
  • Re-refined 2i4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I4J 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 2I4J
  • 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 2I4J, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i4j_A] [2i4j_B] [2i4j]
  • SWISS-PROT database: [P37231]
  • Domain organization of [PPARG_HUMAN] by SWISSPFAM
  • Domain found in 2I4J: [HOLI ] by SMART
  • Other resources with information on 2I4J
  • Community annotation for 2I4J 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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