3KMR Transcription date Nov 11, 2009
title Crystal Structure Of Raralpha Ligand Binding Domain In Compl Agonist Ligand (Am580) And A Coactivator Fragment
authors W.Bourguet, C.Teyssier
compound source
Molecule: Retinoic Acid Receptor Alpha
Chain: A
Fragment: Ligand Binding Domain (Unp Residue 176-421)
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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Nuclear Receptor Coactivator 1
Chain: C
Fragment: Nr Interaction Motif 2 (Unp Residue 686-698)
Synonym: Ncoa-1, Steroid Receptor Coactivator 1, Src-1, Rip Protein Hin-2, Renal Carcinoma Antigen Ny-Ren-52;
Ec: 2.3.1.48
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic
symmetry Space Group: C 1 2 1
R_factor 0.197 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.307 61.218 49.444 90.00 105.38 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand EQN BindingDB enzyme Transferase E.C.2.3.1.48 BRENDA
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] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3kmr.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 3KMR
  • CSU: Contacts of Structural Units for 3KMR
  • Structure Factors (1071 Kb)
  • Retrieve 3KMR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KMR from S2C, [Save to disk]
  • Re-refined 3kmr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KMR 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 3KMR
  • 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 3KMR, from MSDmotif at EBI
  • Fold representative 3kmr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kmr_A] [3kmr] [3kmr_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KMR: [HOLI ] by SMART
  • Alignments of the sequence of 3KMR with the sequences similar proteins can be viewed for 3KMR's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3KMR
  • Community annotation for 3KMR 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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