3KMZ Transcription date Nov 11, 2009
title Crystal Structure Of Raralpha Ligand Binding Domain In Compl The Inverse Agonist Bms493 And A Corepressor Fragment
authors W.Bourguet, A.Le Maire
compound source
Molecule: Retinoic Acid Receptor Alpha
Chain: B, A
Fragment: Ligand Binding Domain
Synonym: Rar-Alpha, Nuclear Receptor Subfamily 1 Group B Me
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1b1, Rara
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Nuclear Receptor Corepressor 1
Chain: C, D
Fragment: Nr1
Synonym: N-Cor1, N-Cor
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic
symmetry Space Group: C 1 2 1
R_factor 0.172 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.831 105.625 53.382 90.00 89.92 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CSO, EQO, GOL enzyme
Primary referenceA unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor., le Maire A, Teyssier C, Erb C, Grimaldi M, Alvarez S, de Lera AR, Balaguer P, Gronemeyer H, Royer CA, Germain P, Bourguet W, Nat Struct Mol Biol. 2010 Jun 13. PMID:20543827
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (3kmz.pdb1.gz) 174 Kb
  • Biological Unit Coordinates (3kmz.pdb2.gz) 173 Kb
  • Biological Unit Coordinates (3kmz.pdb3.gz) 176 Kb
  • LPC: Ligand-Protein Contacts for 3KMZ
  • CSU: Contacts of Structural Units for 3KMZ
  • Structure Factors (506 Kb)
  • Retrieve 3KMZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KMZ from S2C, [Save to disk]
  • Re-refined 3kmz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KMZ 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 3KMZ
  • 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 3KMZ, from MSDmotif at EBI
  • Fold representative 3kmz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kmz_B] [3kmz_C] [3kmz_A] [3kmz] [3kmz_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KMZ: [HOLI ] by SMART
  • Other resources with information on 3KMZ
  • Community annotation for 3KMZ 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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