4DM6 Transcription Protein Binding date Feb 07, 2012
title Crystal Structure Of Rarb Lbd Homodimer In Complex With Ttnp
authors J.Osz, Y.Brelivet, C.Peluso-Iltis, V.Cura, S.Eiler, M.Ruff, W.Bour N.Rochel, D.Moras
compound source
Molecule: Retinoic Acid Receptor Beta
Chain: A, B
Fragment: 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: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Nuclear Receptor Coactivator 1
Chain: E, F
Fragment: Unp Residues 676-700
Synonym: Ncoa-1, Class E Basic Helix-Loop-Helix Protein 74, Protein Hin-2, Rip160, Renal Carcinoma Antigen Ny-Ren-52, S Receptor Coactivator 1, 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 0.206 R_Free 0.239
length a length b length c angle alpha angle beta angle gamma
58.090 84.060 102.140 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand TTB BindingDB enzyme Transferase E.C. BRENDA
A, B

F, E

Primary referenceStructural basis for a molecular allosteric control mechanism of cofactor binding to nuclear receptors., Osz J, Brelivet Y, Peluso-Iltis C, Cura V, Eiler S, Ruff M, Bourguet W, Rochel N, Moras D, Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):E588-94. Epub 2012 Feb 21. PMID:22355136
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (4dm6.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (4dm6.pdb2.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 4DM6
  • CSU: Contacts of Structural Units for 4DM6
  • Structure Factors (373 Kb)
  • Retrieve 4DM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DM6 from S2C, [Save to disk]
  • Re-refined 4dm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DM6 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 4DM6
  • 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 4DM6, from MSDmotif at EBI
  • Fold representative 4dm6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dm6] [4dm6_B] [4dm6_F] [4dm6_E] [4dm6_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DM6: [HOLI ] by SMART
  • Other resources with information on 4DM6
  • Community annotation for 4DM6 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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