1YY4 Transcription date Feb 23, 2005
title Crystal Structure Of Estrogen Receptor Beta Complexed With 1-Chloro-6-(4-Hydroxy-Phenyl)-Naphthalen-2-Ol
authors R.E.Mewshaw, R.J.Edsall Jr., C.Yang, E.S.Manas, Z.B.Xu, R.A.Henderson, J.C.Keith Jr., H.A.Harris
compound source
Molecule: Estrogen Receptor Beta
Chain: A, B
Fragment: Ligand Binding Domain
Synonym: Er-Beta
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Esr2, Estrb, Nr3a2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b

Molecule: Steroid Receptor Coactivator-1
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Was Derived From Steroid Receptor Coactivator-1
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.970 87.677 99.760 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 4NA BindingDB enzyme
Primary referenceERbeta ligands. 3. Exploiting two binding orientations of the 2-phenylnaphthalene scaffold to achieve ERbeta selectivity., Mewshaw RE, Edsall RJ Jr, Yang C, Manas ES, Xu ZB, Henderson RA, Keith JC Jr, Harris HA, J Med Chem. 2005 Jun 16;48(12):3953-79. PMID:15943471
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (1yy4.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 1YY4
  • CSU: Contacts of Structural Units for 1YY4
  • Likely Quarternary Molecular Structure file(s) for 1YY4
  • Retrieve 1YY4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YY4 from S2C, [Save to disk]
  • View 1YY4 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 1YY4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YY4, from MSDmotif at EBI
  • Fold representative 1yy4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yy4_D] [1yy4_B] [1yy4] [1yy4_A] [1yy4_C]
  • SWISS-PROT database: [Q92731] [Q15788]
  • Domain organization of [ESR2_HUMAN] [NCOA1_HUMAN] by SWISSPFAM
  • Domain found in 1YY4: [HOLI ] by SMART
  • Alignments of the sequence of 1YY4 with the sequences similar proteins can be viewed for 1YY4's classification [ESR2_HUMAN] [NCOA1_HUMAN] 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 [ESR2_HUMAN] [NCOA1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YY4
  • Community annotation for 1YY4 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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