5Q0L Transcription date May 31, 2017
title Ligand Binding To Farnesoid-X-Receptor
authors M.G.Rudolph, J.Benz, D.Burger, R.Thoma, A.Ruf, C.Joseph, B.Kuhn, C. H.Yang, S.K.Burley
compound source
Molecule: Bile Acid Receptor
Chain: A, C
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
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Coactivator Peptide Src-1 Hd3
Chain: B, D
Fragment: Unp Residues 744-757
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 2 2 21
R_factor 0.209 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.847 82.960 188.971 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 9KY, MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceD3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies., Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE, J Comput Aided Mol Des. 2017 Dec 4. pii: 10.1007/s10822-017-0088-4. doi:, 10.1007/s10822-017-0088-4. PMID:29204945
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (5q0l.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (5q0l.pdb2.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 5Q0L
  • CSU: Contacts of Structural Units for 5Q0L
  • Structure Factors (687 Kb)
  • Retrieve 5Q0L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Q0L from S2C, [Save to disk]
  • Re-refined 5q0l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5Q0L 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 5Q0L
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5q0l_A] [5q0l_D] [5q0l_B] [5q0l_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Q0L
  • Community annotation for 5Q0L at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science