1XAP Transcription date Aug 26, 2004
title Structure Of The Ligand Binding Domain Of The Retinoic Acid Beta
authors P.Germain, S.Kammerer, C.Peluso-Iltis, D.Tortolani, F.C.Zusi, J.S P.Lapointe, J.P.Daris, A.Marinier, A.R.De Lera, N.Rochel, H.Gron
compound source
Molecule: Retinoic Acid Receptor Beta
Chain: A
Fragment: Ligand Binding Domain
Synonym: Rar-Beta, Rar-Epsilon, Hbv-Activated Protein
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.213 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
47.276 57.808 90.289 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand TTB BindingDB enzyme
related structures by homologous chain: 2LBD, 3LBD

Primary referenceRational design of RAR-selective ligands revealed by RARbeta crystal stucture., Germain P, Kammerer S, Perez E, Peluso-Iltis C, Tortolani D, Zusi FC, Starrett J, Lapointe P, Daris JP, Marinier A, de Lera AR, Rochel N, Gronemeyer H, EMBO Rep 2004 Sep;5(9):877-82. PMID:15319780
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1xap.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 1XAP
  • CSU: Contacts of Structural Units for 1XAP
  • Likely Quarternary Molecular Structure file(s) for 1XAP
  • Structure Factors (219 Kb)
  • Retrieve 1XAP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XAP from S2C, [Save to disk]
  • Re-refined 1xap structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XAP 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 1XAP
  • 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 1XAP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xapa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1xap from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xap] [1xap_A]
  • SWISS-PROT database: [P10826]
  • Domain organization of [RARB_HUMAN] by SWISSPFAM
  • Domain found in 1XAP: [HOLI ] by SMART
  • Other resources with information on 1XAP
  • Community annotation for 1XAP 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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