2LBD Nuclear Receptor date Aug 19, 1997
title Ligand-Binding Domain Of The Human Retinoic Acid Receptor Ga To All-Trans Retinoic Acid
authors J.P.Renaud, N.Rochel, M.Ruff, D.Moras, Structural Proteomics In (Spine)
compound source
Molecule: Retinoic Acid Receptor Gamma
Chain: A
Fragment: Lbd (Ligand-Binding Domain), Residues 178 - 423
Synonym: E Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Bl21
Cellular_location: Nucleus
Gene: Human Rar Gamma A Cdna (Nucleotides 946 - 1683)
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_cellular_location: Cytoplasm
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
Expression_system_gene: Hrargamma
Other_details: Cdna Cloning\: Krust Et Al., Proc.Natl.Acad. 86,5310-5314,1989
symmetry Space Group: P 41 21 2
R_factor 0.210 R_Free 0.313
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.600 60.600 155.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.06 Å
ligand REA BindingDB enzyme
related structures by homologous chain: 1EXX, 1XAP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid., Renaud JP, Rochel N, Ruff M, Vivat V, Chambon P, Gronemeyer H, Moras D, Nature 1995 Dec 14;378(6558):681-9. PMID:7501014
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (2lbd.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 2LBD
  • CSU: Contacts of Structural Units for 2LBD
  • Likely Quarternary Molecular Structure file(s) for 2LBD
  • Structure Factors (123 Kb)
  • Retrieve 2LBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2LBD from S2C, [Save to disk]
  • Re-refined 2lbd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2LBD 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 2LBD
  • 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 2LBD, from MSDmotif at EBI
  • Genome occurence of 2LBD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2lbd__, region [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2lbd_A] [2lbd]
  • SWISS-PROT database: [P13631]
  • Domain organization of [RARG_HUMAN] by SWISSPFAM
  • Domain found in 2LBD: [HOLI ] by SMART
  • Other resources with information on 2LBD
  • Community annotation for 2LBD 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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