3GYU Transcription date Apr 05, 2009
title Nuclear Receptor Daf-12 From Parasitic Nematode Strongyloide Stercoralis In Complex With Its Physiological Ligand Dafach Delta 7
authors X.E.Zhou, Z.Wang, K.Suino-Powell, D.L.Motola, A.Conneely, C.Ogata K.K.Sharma, R.J.Auchus, S.A.Kliewer, H.E.Xu, D.J.Mangelsdorf
compound source
Molecule: Nuclear Hormone Receptor Of The Steroidthyroid H Receptors Superfamily;
Chain: A
Fragment: Ligand Binding Domain
Engineered: Yes
 Organism_scientific: Strongyloides Stercoralis
Organism_taxid: 6248
Gene: Daf-12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24a

Molecule: Src1
Chain: B
Fragment: Nuclear Receptor Binding Motif 4
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 65
R_factor 0.208 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.946 120.946 40.757 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand DL7, MSE enzyme
Primary referenceIdentification of the nuclear receptor DAF-12 as a therapeutic target in parasitic nematodes., Wang Z, Zhou XE, Motola DL, Gao X, Suino-Powell K, Conneely A, Ogata C, Sharma KK, Auchus RJ, Lok JB, Hawdon JM, Kliewer SA, Xu HE, Mangelsdorf DJ, Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9138-43. Epub 2009 Jun 2. PMID:19497877
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (3gyu.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 3GYU
  • CSU: Contacts of Structural Units for 3GYU
  • Likely Quarternary Molecular Structure file(s) for 3GYU
  • Structure Factors (293 Kb)
  • Retrieve 3GYU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GYU from S2C, [Save to disk]
  • Re-refined 3gyu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3GYU 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 3GYU
  • 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 3GYU, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gyu] [3gyu_A] [3gyu_B]
  • SWISS-PROT database: [Q9XZJ5]
  • Domain organization of [Q9XZJ5_9BILA] by SWISSPFAM
  • Domain found in 3GYU: [HOLI ] by SMART
    • Other resources with information on 3GYU
  • Community annotation for 3GYU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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