5Q1G 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
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
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 0.205 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.525 161.647 110.049 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 9NM enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


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] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (5q1g.pdb1.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 5Q1G
  • CSU: Contacts of Structural Units for 5Q1G
  • Structure Factors (697 Kb)
  • Retrieve 5Q1G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Q1G from S2C, [Save to disk]
  • Re-refined 5q1g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5Q1G 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 5Q1G
  • 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: [5q1g_A] [5q1g_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Q1G
  • Community annotation for 5Q1G at PDBWiki (http://pdbwiki.org)

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