2Q59 Ligand Binding Protein date May 31, 2007
title Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl
authors J.B.Bruning, K.W.Nettles
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: A
Fragment: Ligand Binding Domain
Synonym: Ppar-Gamma
Engineered: Yes
Other_details: Cys A 285 Is 2-Hydroxyethylated
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg19

Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: B
Fragment: Ligand Binding Domain
Synonym: Ppar-Gamma
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg19
symmetry Space Group: C 1 2 1
R_factor 0.183 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.161 63.939 119.187 90.00 103.43 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 240, CME BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referencePartial Agonists Activate PPARgamma Using a Helix 12 Independent Mechanism., Bruning JB, Chalmers MJ, Prasad S, Busby SA, Kamenecka TM, He Y, Nettles KW, Griffin PR, Structure. 2007 Oct;15(10):1258-71. PMID:17937915
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (2q59.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 2Q59
  • CSU: Contacts of Structural Units for 2Q59
  • Likely Quarternary Molecular Structure file(s) for 2Q59
  • Structure Factors (265 Kb)
  • Retrieve 2Q59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q59 from S2C, [Save to disk]
  • Re-refined 2q59 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q59 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 2Q59
  • 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
  • 3D motif for 2Q59, from MSDmotif at EBI
  • Fold representative 2q59 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q59] [2q59_B] [2q59_A]
  • SWISS-PROT database: [P37231]
  • Domain organization of [PPARG_HUMAN] by SWISSPFAM
  • Domain found in 2Q59: [HOLI ] by SMART
  • Other resources with information on 2Q59
  • Community annotation for 2Q59 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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