3VSP Transcription date Apr 30, 2012
title Human Ppar Gamma Ligand Binding Domain In Complex With A Gam Selective Agonist Mekt28
authors T.Oyama, T.Waku, M.Ohashi, K.Morikawa, H.Miyachi
compound source
Molecule: Peroxisome Proliferator-Activated Receptor Gamma
Chain: A, B
Fragment: Ligand Binding Domain
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_strain: Bl21(E3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.409 60.871 118.598 90.00 102.95 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand EK8 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 (3vsp.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (3vsp.pdb2.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 3VSP
  • CSU: Contacts of Structural Units for 3VSP
  • Structure Factors (531 Kb)
  • Retrieve 3VSP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VSP from S2C, [Save to disk]
  • Re-refined 3vsp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3VSP 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 3VSP
  • 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 3VSP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vsp_A] [3vsp_B] [3vsp]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VSP: [HOLI ] by SMART
    • Other resources with information on 3VSP
  • Community annotation for 3VSP at PDBWiki (http://pdbwiki.org)

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