5DKB Transcription date Sep 03, 2015
title Crystal Structure Of The Er-Alpha Ligand-Binding Domain In C With A 3-Methylphenylamino-Substituted Ethyl Triaryl-Ethyle Derivative 4,4'-(2-{3-[(3-Methylphenyl)Amino]Phenyl}But-1-E Diyl)Diphenol
authors J.C.Nwachukwu, S.Srinivasan, Y.Zheng, S.Wang, J.Min, C.Dong, Z.Lia V.Cavett, J.Nowak, R.Houtman, K.E.Carlson, J.S.Josan, O.Elemento J.A.Katzenellenbogen, H.B.Zhou, K.W.Nettles
compound source
Molecule: Estrogen Receptor
Chain: A, B
Fragment: Ligand-Binding Domain
Synonym: Er,Er-Alpha,Estradiol Receptor,Nuclear Receptor Su Group A Member 1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Esr1, Esr, Nr3a1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Nuclear Receptor Coactivator 2
Chain: C, D
Fragment: Nuclear Receptor-Interacting Peptide
Synonym: Ncoa-2,Class E Basic Helix-Loop-Helix Protein 75,B Transcriptional Intermediary Factor 2,Htif2;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.183 R_Free 0.226
length a length b length c angle alpha angle beta angle gamma
56.347 82.844 58.458 90.00 111.32 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 5C9 enzyme
Primary referencePredictive features of ligand-specific signaling through the estrogen receptor., Nwachukwu JC, Srinivasan S, Zheng Y, Wang S, Min J, Dong C, Liao Z, Nowak J, Wright NJ, Houtman R, Carlson KE, Josan JS, Elemento O, Katzenellenbogen JA, Zhou HB, Nettles KW, Mol Syst Biol. 2016 Apr 22;12(4):864. doi: 10.15252/msb.20156701. PMID:27107013
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (5dkb.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 5DKB
  • CSU: Contacts of Structural Units for 5DKB
  • Structure Factors (217 Kb)
  • Retrieve 5DKB in mmCIF format [Save to disk]
  • Re-refined 5dkb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DKB 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 5DKB
  • 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
  • Fold representative 5dkb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dkb_B] [5dkb_D] [5dkb] [5dkb_C] [5dkb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DKB: [HOLI ] by SMART
  • Other resources with information on 5DKB
  • Community annotation for 5DKB at PDBWiki (http://pdbwiki.org)

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