4LBD Nuclear Receptor date Feb 04, 1998
title Ligand-Binding Domain Of The Human Retinoic Acid Receptor Ga To The Synthetic Agonist Bms961
authors B.P.Klaholz, J.P.Renaud, A.Mitschler, D.Moras, Structural Prote Europe (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: Cytoplasm
Gene: Hrargamma
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pet-15b
symmetry Space Group: P 41 21 2
R_factor 0.183 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.882 59.882 155.958 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 961 enzyme
related structures by homologous chain: 1DKF, 3LBD
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceConformational adaptation of agonists to the human nuclear receptor RAR gamma., Klaholz BP, Renaud JP, Mitschler A, Zusi C, Chambon P, Gronemeyer H, Moras D, Nat Struct Biol 1998 Mar;5(3):199-202. PMID:9501913
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (4lbd.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 4LBD
  • CSU: Contacts of Structural Units for 4LBD
  • Likely Quarternary Molecular Structure file(s) for 4LBD
  • Retrieve 4LBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4LBD from S2C, [Save to disk]
  • View 4LBD 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 4LBD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4LBD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d4lbd__, 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: [4lbd] [4lbd_A]
  • SWISS-PROT database: [P13631]
  • Domain organization of [RARG_HUMAN] by SWISSPFAM
  • Domain found in 4LBD: [HOLI ] by SMART
  • Other resources with information on 4LBD
  • Community annotation for 4LBD 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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