2GTK Transcription Regulator date Apr 28, 2006
title Structure-Based Design Of Indole Propionic Acids As Novel Pp Agonists
authors B.Kuhn, H.Hilpert, J.Benz, A.Binggeli, U.Grether, R.Humm, H.P.Mae M.Meyer, P.Mohr
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: A
Synonym: Pparg-Lbd; 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

Molecule: Decamer From Nuclear Receptor Coactivator 1
Chain: B
Fragment: Residues 631-640
Engineered: Yes
Other_details: Full Protein Is Transferase, 2.3.1.48

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Homo Sapie
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.239 68.319 87.952 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 208 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure-based design of indole propionic acids as novel PPARalpha/gamma co-agonists., Kuhn B, Hilpert H, Benz J, Binggeli A, Grether U, Humm R, Marki HP, Meyer M, Mohr P, Bioorg Med Chem Lett. 2006 Aug 1;16(15):4016-20. Epub 2006 Jun 5. PMID:16737814
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (2gtk.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 2GTK
  • CSU: Contacts of Structural Units for 2GTK
  • Likely Quarternary Molecular Structure file(s) for 2GTK
  • Structure Factors (145 Kb)
  • Retrieve 2GTK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GTK from S2C, [Save to disk]
  • Re-refined 2gtk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2GTK 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 2GTK
  • 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 2GTK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gtk_B] [2gtk] [2gtk_A]
  • SWISS-PROT database: [Q15788] [P37231]
  • Domain organization of [NCOA1_HUMAN] [PPARG_HUMAN] by SWISSPFAM
  • Domain found in 2GTK: [HOLI ] by SMART
  • Other resources with information on 2GTK
  • Community annotation for 2GTK 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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