5KCD Transcription date Jun 06, 2016
title Crystal Structure Of The Er-Alpha Ligand-Binding Domain (Y53 Complex With An N-Methyl Substituted Obhs-N Derivative
authors J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, V.Dharmarajan, D.Goswami I.Kastrati, S.Novick, J.Nowak, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Mi J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, J.A.Katzenellenbo 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: Ncoa2
Chain: C, D
Fragment: Nuclear Receptor-Interacting Peptide
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans
symmetry Space Group: P 1 21 1
R_factor 0.177 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.945 83.463 58.779 90.00 109.38 90.00
method X-Ray Diffractionresolution 1.82 Å
ligand OB2 enzyme
note 5KCD supersedes 4ZUC
Primary referenceFull antagonism of the estrogen receptor without a prototypical ligand side chain., Srinivasan S, Nwachukwu JC, Bruno NE, Dharmarajan V, Goswami D, Kastrati I, Novick S, Nowak J, Cavett V, Zhou HB, Boonmuen N, Zhao Y, Min J, Frasor J, Katzenellenbogen BS, Griffin PR, Katzenellenbogen JA, Nettles KW, Nat Chem Biol. 2017 Jan;13(1):111-118. doi: 10.1038/nchembio.2236. Epub 2016 Nov , 21. PMID:27870835
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (171 Kb) [Save to disk]
  • Biological Unit Coordinates (5kcd.pdb1.gz) 164 Kb
  • LPC: Ligand-Protein Contacts for 5KCD
  • CSU: Contacts of Structural Units for 5KCD
  • Structure Factors (534 Kb)
  • Retrieve 5KCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KCD from S2C, [Save to disk]
  • Re-refined 5kcd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KCD 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 5KCD
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kcd_A] [5kcd_D] [5kcd] [5kcd_B] [5kcd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5KCD: [HOLI ] by SMART
  • Other resources with information on 5KCD
  • Community annotation for 5KCD at PDBWiki (http://pdbwiki.org)

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