1DKF Hormone Growth Factor Receptor date Dec 07, 1999
title Crystal Structure Of A Heterodimeric Complex Of Rar And Rxr Ligand-Binding Domains
authors W.Bourguet, V.Vivat, J.M.Wurtz, P.Chambon, H.Gronemeyer, D.Moras, Structural Proteomics In Europe (Spine)
compound source
Molecule: Protein (Retinoid X Receptor-Alpha)
Chain: A
Fragment: Ligand-Binding Domain
Synonym: Rxr-Alpha
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Protein (Retinoic Acid Receptor-Alpha)
Chain: B
Fragment: Ligand-Binding Domain
Synonym: Rar-Alpha
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 61 2 2
R_factor 0.203 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.600 116.600 207.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand BMS, OLA enzyme
related structures by homologous chain: 1G1U, 1RDT, 1XDK, 4LBD
Primary referenceCrystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains., Bourguet W, Vivat V, Wurtz JM, Chambon P, Gronemeyer H, Moras D, Mol Cell 2000 Feb;5(2):289-98. PMID:10882070
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (1dkf.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 1DKF
  • CSU: Contacts of Structural Units for 1DKF
  • Likely Quarternary Molecular Structure file(s) for 1DKF
  • Structure Factors (210 Kb)
  • Retrieve 1DKF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DKF from S2C, [Save to disk]
  • Re-refined 1dkf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DKF 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 1DKF
  • 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 1DKF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dkfa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dkfb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1dkf 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: [1dkf] [1dkf_B] [1dkf_A]
  • SWISS-PROT database: [P10276] [P28700]
  • Domain organization of [RARA_HUMAN] [RXRA_MOUSE] by SWISSPFAM
  • Domain found in 1DKF: [HOLI ] by SMART
  • Alignments of the sequence of 1DKF with the sequences similar proteins can be viewed for 1DKF's classification [RARA_HUMAN] [RXRA_MOUSE] 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 [RARA_HUMAN] [RXRA_MOUSE] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DKF
  • Community annotation for 1DKF 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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