3GD2 Transcription Transcription Activator date Feb 23, 2009
title Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr)
authors K.P.Madauss, S.P.Williams, D.N.Deaton, G.B.Wisely, R.B.Mcfadyen
compound source
Molecule: Bile Acid Receptor
Chain: A
Fragment: Farsenoid X Receptor
Synonym: Farnesoid X-Activated Receptor, Farnesol Receptor Nuclear Receptor Subfamily 1 Group H Member 4, Retinoid X R Interacting Protein 14, Rxr-Interacting Protein 14;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1h4, Bar, Fxr, Hrr1, Rip14
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Activator Peptide
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: F 2 3
R_factor 0.238 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
158.749 158.749 158.749 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand 708 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSubstituted isoxazole analogs of farnesoid X receptor (FXR) agonist GW4064., Bass JY, Caldwell RD, Caravella JA, Chen L, Creech KL, Deaton DN, Madauss KP, Marr HB, McFadyen RB, Miller AB, Parks DJ, Todd D, Williams SP, Wisely GB, Bioorg Med Chem Lett. 2009 Jun 1;19(11):2969-73. Epub 2009 Apr 18. PMID:19410460
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (3gd2.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3GD2
  • CSU: Contacts of Structural Units for 3GD2
  • Likely Quarternary Molecular Structure file(s) for 3GD2
  • Structure Factors (85 Kb)
  • Retrieve 3GD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GD2 from S2C, [Save to disk]
  • Re-refined 3gd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GD2 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 3GD2
  • 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 3GD2, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gd2_A] [3gd2_B] [3gd2]
  • SWISS-PROT database: [Q96RI1]
  • Domain organization of [NR1H4_HUMAN] by SWISSPFAM
  • Domain found in 3GD2: [HOLI ] by SMART
  • Other resources with information on 3GD2
  • Community annotation for 3GD2 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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