5DKS Transcription date Sep 03, 2015
title Crystal Structure Of The Er-Alpha Ligand-Binding Domain In C With A 2-Naphthylamino-Substituted, Ethyl, Triaryl-Ethylene Derivative 4,4'-{2-[3-(Naphthalen-1-Ylamino)Phenyl]But-1-En 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 0.213 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
54.540 82.750 58.150 90.00 110.83 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 5C6 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] (167 Kb) [Save to disk]
  • Biological Unit Coordinates (5dks.pdb1.gz) 158 Kb
  • LPC: Ligand-Protein Contacts for 5DKS
  • CSU: Contacts of Structural Units for 5DKS
  • Structure Factors (129 Kb)
  • Retrieve 5DKS in mmCIF format [Save to disk]
  • Re-refined 5dks structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DKS 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 5DKS
  • 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 5dks from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dks] [5dks_A] [5dks_B] [5dks_D] [5dks_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DKS: [HOLI ] by SMART
  • Other resources with information on 5DKS
  • Community annotation for 5DKS at PDBWiki (http://pdbwiki.org)

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