1KNU Dna Binding Protein date Dec 19, 2001
title Ligand Binding Domain Of The Human Peroxisome Proliferator A Receptor Gamma In Complex With A Synthetic Agonist
authors L.A.Svensson, S.B.Mortensen, J.Fleckner, H.F.Woeldike
compound source
Molecule: Peroxisome Proliferator Activated Receptor Gamma
Chain: A, B
Fragment: Ligand Binding Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Adipose Tissue
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-3x-Hpparglbd
symmetry Space Group: C 1 2 1
R_factor 0.224 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
92.270 63.440 119.240 90.00 101.84 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand YPA BindingDB enzyme
related structures by homologous chain: 1GWX, 1M2Z, 3GWX
A, B

Primary referenceNovel tricyclic-alpha-alkyloxyphenylpropionic acids: dual PPARalpha/gamma agonists with hypolipidemic and antidiabetic activity., Sauerberg P, Pettersson I, Jeppesen L, Bury PS, Mogensen JP, Wassermann K, Brand CL, Sturis J, Woldike HF, Fleckner J, Andersen AS, Mortensen SB, Svensson LA, Rasmussen HB, Lehmann SV, Polivka Z, Sindelar K, Panajotova V, Ynddal L, Wulff EM, J Med Chem 2002 Feb 14;45(4):789-804. PMID:11831892
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (1knu.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 1KNU
  • CSU: Contacts of Structural Units for 1KNU
  • Likely Quarternary Molecular Structure file(s) for 1KNU
  • Structure Factors (229 Kb)
  • Retrieve 1KNU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KNU from S2C, [Save to disk]
  • Re-refined 1knu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KNU 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 1KNU
  • 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 1KNU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1knua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1knub_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1knu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1knu_B] [1knu_A] [1knu]
  • SWISS-PROT database: [P37231]
  • Domain organization of [PPARG_HUMAN] by SWISSPFAM
  • Domain found in 1KNU: [HOLI ] by SMART
  • Other resources with information on 1KNU
  • Community annotation for 1KNU 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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