1NYX Transcription date Feb 14, 2003
title Ligand Binding Domain Of The Human Peroxisome Proliferator Activated Receptor Gamma In Complex With An Agonist
authors S.Ebdrup, I.Pettersson, H.B.Rasmussen, H.J.Deussen, A.Frost Jensen, S.B.Mortensen, J.Fleckner, L.Pridal, L.Nygaard, P.Sauerberg
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
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-3x
symmetry Space Group: C 1 2 1
R_factor 0.237 R_Free 0.306
length a length b length c angle alpha angle beta angle gamma
91.546 62.090 117.741 90.00 102.91 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand DRF BindingDB enzyme
related structures by homologous chain: 1WM0, 1Y0S
A, B

Primary referenceSynthesis and biological and structural characterization of the dual-acting peroxisome proliferator-activated receptor alpha/gamma agonist ragaglitazar., Ebdrup S, Pettersson I, Rasmussen HB, Deussen HJ, Frost Jensen A, Mortensen SB, Fleckner J, Pridal L, Nygaard L, Sauerberg P, J Med Chem 2003 Apr 10;46(8):1306-17. PMID:12672231
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (1nyx.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 1NYX
  • CSU: Contacts of Structural Units for 1NYX
  • Likely Quarternary Molecular Structure file(s) for 1NYX
  • Retrieve 1NYX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NYX from S2C, [Save to disk]
  • View 1NYX 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 1NYX
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NYX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nyxa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nyxb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1nyx 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: [1nyx_B] [1nyx_A] [1nyx]
  • SWISS-PROT database: [P37231]
  • Domain organization of [PPARG_HUMAN] by SWISSPFAM
  • Domain found in 1NYX: [HOLI ] by SMART
  • Other resources with information on 1NYX
  • Community annotation for 1NYX 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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