1RDT Hormone Growth Factor date Nov 06, 2003
title Crystal Structure Of A New Rexinoid Bound To The Rxralpha Ligand Binding Doamin In The Rxralphappargamma Heterodimer
authors C.D.Haffner, J.M.Lenhard, A.B.Miller, D.L.Mcdougald, K.Dwornik, O.R.Ittoop, R.T.Gampe Jr., H.E.Xu, S.Blanchard, V.G.Montana
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A
Fragment: Ligand Binding Doamin
Synonym: Rxralpha
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rxra, Nr2b1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacyc184

Molecule: Lxxll Motif Coactivator
Chain: B
Fragment: Lxxll Peptide
Engineered: Yes

Synthetic: Yes

Molecule: Peroxisome Proliferator Activated Receptor Gamma
Chain: D
Fragment: Ligand Binding Doamin
Synonym: Ppar-Gamma
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pparg, Nr1c3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset

Molecule: Lxxll Motif Coactivator
Chain: E
Fragment: Lxxll Peptide
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.690 54.580 211.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 570, L79 BindingDB enzyme
related structures by homologous chain: 1DKF, 1I7I, 1K74, 3GWX
Gene
Ontology
ChainFunctionProcessComponent
A


B


D


Primary referenceStructure-based design of potent retinoid X receptor alpha agonists., Haffner CD, Lenhard JM, Miller AB, McDougald DL, Dwornik K, Ittoop OR, Gampe RT Jr, Xu HE, Blanchard S, Montana VG, Consler TG, Bledsoe RK, Ayscue A, Croom D, J Med Chem 2004 Apr 8;47(8):2010-29. PMID:15056000
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (1rdt.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 1RDT
  • CSU: Contacts of Structural Units for 1RDT
  • Likely Quarternary Molecular Structure file(s) for 1RDT
  • Retrieve 1RDT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RDT from S2C, [Save to disk]
  • View 1RDT 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 1RDT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1RDT, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rdta_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rdtd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1rdt from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1rdt_D] [1rdt_E] [1rdt] [1rdt_A] [1rdt_B]
  • SWISS-PROT database: [Q15788] [P37231] [P19793]
  • Domain organization of [NCOA1_HUMAN] [PPARG_HUMAN] [RXRA_HUMAN] by SWISSPFAM
  • Domain found in 1RDT: [HOLI ] by SMART
  • Other resources with information on 1RDT
  • Community annotation for 1RDT 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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