4WVD Transcription date Nov 05, 2014
title Identification Of A Novel Fxr Ligand That Regulates Metaboli
authors R.Wang, Y.Li
compound source
Molecule: Nuclear Receptor Corepressor 1
Chain: C, D
Fragment: Unp Residues 2259-2275
Synonym: N-Cor1
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Bile Acid Receptor
Chain: A, B
Fragment: Ligand Binding Domain, Unp Residues 244-454
Synonym: Farnesoid X-Activated Receptor,Farnesol Receptor H Nuclear Receptor Subfamily 1 Group H Member 4,Retinoid X Re Interacting Protein 14,Rxr-Interacting Protein 14;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1h4, Bar, Fxr, Hrr1, Rip14
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24
symmetry Space Group: I 21 21 21
R_factor 0.277 R_Free 0.302
length a length b length c angle alpha angle beta angle gamma
53.008 161.759 169.018 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand FMT, IVM enzyme
note 4WVD supersedes 4II6
A, B

Primary referenceThe antiparasitic drug ivermectin is a novel FXR ligand that regulates metabolism., Jin L, Feng X, Rong H, Pan Z, Inaba Y, Qiu L, Zheng W, Lin S, Wang R, Wang Z, Wang S, Liu H, Li S, Xie W, Li Y, Nat Commun. 2013;4:1937. doi: 10.1038/ncomms2924. PMID:23728580
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (4wvd.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (4wvd.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 4WVD
  • CSU: Contacts of Structural Units for 4WVD
  • Structure Factors (310 Kb)
  • Retrieve 4WVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4WVD from S2C, [Save to disk]
  • Re-refined 4wvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4WVD 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 4WVD
  • 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 4WVD, from MSDmotif at EBI
  • Fold representative 4wvd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4wvd_A] [4wvd] [4wvd_D] [4wvd_C] [4wvd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4WVD: [HOLI ] by SMART
  • Other resources with information on 4WVD
  • Community annotation for 4WVD at PDBWiki (http://pdbwiki.org)

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