4K6I Transcription date Apr 15, 2013
title Crystal Structure Of Human Retinoid X Receptor Alpha-Ligand Domain Complex With Targretin And The Coactivator Peptide G
authors G.Xia, C.D.Smith, D.D.Muccio
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A
Fragment: Ligand Binding Domain, Unp Residues 228-458
Synonym: Nuclear Receptor Subfamily 2 Group B Member 1, Ret Receptor Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: P19793
Gene: Nr2b1, Rxra, Rxra Nr2b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Bl21(De3)

Molecule: Nuclear Receptor Coactivator 2
Chain: B
Fragment: Coactivator Peptide, Unp Residues 686-698
Synonym: Ncoa-2, Class E Basic Helix-Loop-Helix Protein 75, Transcriptional Intermediary Factor 2, Htif2;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Grip-1 From Anaspec Inc
symmetry Space Group: P 43 21 2
R_factor 0.246 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.150 68.150 106.590 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 9RA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDefining the communication between agonist and coactivator binding in the retinoid X receptor ligand binding domain., Boerma LJ, Xia G, Qui C, Cox BD, Chalmers MJ, Smith CD, Lobo-Ruppert S, Griffin P, Muccio DD, Renfrow MB, J Biol Chem. 2013 Nov 1. PMID:24187139
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (4k6i.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 4K6I
  • CSU: Contacts of Structural Units for 4K6I
  • Structure Factors (368 Kb)
  • Retrieve 4K6I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4K6I from S2C, [Save to disk]
  • Re-refined 4k6i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4K6I 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 4K6I
  • 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
  • 3D motif for 4K6I, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4k6i] [4k6i_A] [4k6i_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4K6I: [HOLI ] by SMART
  • Other resources with information on 4K6I
  • Community annotation for 4K6I at PDBWiki (http://pdbwiki.org)

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