3V9T Transcription Transcription Regulator date Dec 28, 2011
title Crystal Structure Of The Ppargamma-Lbd Complexed With A Cerc Derivative Modulator
authors Y.Matsui, H.Hanzawa
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: A
Fragment: Ligand Binding Domain, Unp Residues 234-505
Synonym: Ppar-Gamma, Nuclear Receptor Subfamily 1 Group C M
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_vector_type: Plasmid

Molecule: Peptide From Peroxisome Proliferator-Activated Re Gamma Coactivator 1-Alpha;
Chain: C
Synonym: Pgc-1-Alpha, Ppar-Gamma Coactivator 1-Alpha, Pparg Ligand Effect Modulator 6;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.219
length a length b length c angle alpha angle beta angle gamma
38.889 54.614 66.797 90.00 92.35 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand 17L BindingDB enzyme

Primary referenceSubstituents at the naphthalene C3 position of (-)-Cercosporamide derivatives significantly affect the maximal efficacy as PPARgamma partial agonists., Furukawa A, Arita T, Fukuzaki T, Satoh S, Mori M, Honda T, Matsui Y, Wakabayashi K, Hayashi S, Araki K, Ohsumi J, Bioorg Med Chem Lett. 2012 Feb 1;22(3):1348-51. Epub 2011 Dec 16. PMID:22225641
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (3v9t.pdb1.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 3V9T
  • CSU: Contacts of Structural Units for 3V9T
  • Structure Factors (407 Kb)
  • Retrieve 3V9T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V9T from S2C, [Save to disk]
  • Re-refined 3v9t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V9T 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 3V9T
  • 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 3V9T, from MSDmotif at EBI
  • Fold representative 3v9t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v9t_C] [3v9t_A] [3v9t]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3V9T: [HOLI ] by SMART
  • Other resources with information on 3V9T
  • Community annotation for 3V9T at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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