4JYG Transcription Agonist date Mar 29, 2013
title Crystal Structure Of Rarbeta Lbd In Complex With Agonist Bms {[(5,5-Dimethyl-8-Phenyl-5,6-Dihydronaphthalen-2-Yl) Carbonyl]Amino}Benzoic Acid]
authors E.K.Nadendla, C.Teyssier, P.Germain, V.Delfosse, W.Bourguet
compound source
Molecule: Retinoic Acid Receptor Beta
Chain: A, B
Fragment: Ligand Binding Domain, Unp Residues 176-421
Synonym: Rar-Beta, Hbv-Activated Protein, Nuclear Receptor Group B Member 2, Rar-Epsilon;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rarb, Hap, Nr1b2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21-De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Steroid Receptor Coactivator 1
Chain: F, G
Fragment: Unp Residues 686-698
Synonym: Src-1
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.199 R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
58.240 84.830 108.420 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand 1NY, FLC, PE4 enzyme Transferase E.C. BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (4jyg.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 4JYG
  • CSU: Contacts of Structural Units for 4JYG
  • Structure Factors (172 Kb)
  • Retrieve 4JYG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JYG from S2C, [Save to disk]
  • Re-refined 4jyg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JYG 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 4JYG
  • 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 4JYG, from MSDmotif at EBI
  • Fold representative 4jyg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jyg_F] [4jyg_B] [4jyg_A] [4jyg] [4jyg_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4JYG: [HOLI ] by SMART
  • Other resources with information on 4JYG
  • Community annotation for 4JYG at PDBWiki (http://pdbwiki.org)

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