3A9E Transcription date Oct 24, 2009
title Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And Ant Bound Rxr-Alpha Heterodimer Ligand Binding Domains
authors Y.Sato, S.Duclaud, C.Peluso-Iltis, P.Poussin, D.Moras, N.Rochel
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A
Fragment: Ligand Binding Domain
Synonym: Retinoid X Receptor Alpha, Nuclear Receptor Subfam Group B Member 1;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rxra, Nr2b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Retinoic Acid Receptor Alpha
Chain: B
Fragment: Ligand Binding Domain
Synonym: Rar-Alpha, Nuclear Receptor Subfamily 1 Group B Me
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rara, Nr1b1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: 13-Mer (Lxxll Motif) From Nuclear Receptor Coacti
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 43 21 2
R_factor 0.201 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.300 105.300 111.338 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand 754, REA BindingDB enzyme
Primary referenceThe "Phantom Effect" of the Rexinoid LG100754: structural and functional insights., Sato Y, Ramalanjaona N, Huet T, Potier N, Osz J, Antony P, Peluso-Iltis C, Poussin-Courmontagne P, Ennifar E, Mely Y, Dejaegere A, Moras D, Rochel N, PLoS One. 2010 Nov 30;5(11):e15119. doi: 10.1371/journal.pone.0015119. PMID:21152046
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (170 Kb) [Save to disk]
  • Biological Unit Coordinates (3a9e.pdb1.gz) 164 Kb
  • Biological Unit Coordinates (3a9e.pdb2.gz) 326 Kb
  • LPC: Ligand-Protein Contacts for 3A9E
  • CSU: Contacts of Structural Units for 3A9E
  • Structure Factors (140 Kb)
  • Retrieve 3A9E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A9E from S2C, [Save to disk]
  • Re-refined 3a9e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A9E 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 3A9E
  • 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 3A9E, from MSDmotif at EBI
  • Fold representative 3a9e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a9e] [3a9e_B] [3a9e_A] [3a9e_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3A9E: [HOLI ] by SMART
  • Alignments of the sequence of 3A9E with the sequences similar proteins can be viewed for 3A9E's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3A9E
  • Community annotation for 3A9E at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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