3OMO Protein Binding date Aug 27, 2010
title Fragment-Based Design Of Novel Estrogen Receptor Ligands
authors S.Moecklinghoff, W.A.Van Otterlo, R.Rose, S.Fuchs, M.Dominguez S H.Waldmann, C.Ottmann, L.Brunsveld
compound source
Molecule: Estrogen Receptor Beta
Chain: A, B
Fragment: Ligand Binding Domain (Unp Residues 261-500)
Synonym: Er-Beta, Nuclear Receptor Subfamily 3 Group A Memb
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Esr2, Estrb, Nr3a2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nuclear Receptor Coactivator 1
Chain: C, D
Fragment: Box 2 (Unp Residues 683-701)
Synonym: Ncoa-1, Steroid Receptor Coactivator 1, Src-1, Rip Protein Hin-2, Renal Carcinoma Antigen Ny-Ren-52, Class E B Helix-Loop-Helix Protein 74, Bhlhe74;
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: P 31
R_factor 0.208 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
70.570 70.570 109.990 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.21 Å
ligand WV7 BindingDB enzyme
A, B

Primary referenceDesign and Evaluation of Fragment-Like Estrogen Receptor Tetrahydroisoquinoline Ligands from a Scaffold-Detection Approach., Mocklinghoff S, van Otterlo WA, Rose R, Fuchs S, Zimmermann TJ, Dominguez Seoane M, Waldmann H, Ottmann C, Brunsveld L, J Med Chem. 2011 Mar 7. PMID:21381753
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (3omo.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (3omo.pdb2.gz) 42 Kb
  • Biological Unit Coordinates (3omo.pdb3.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 3OMO
  • CSU: Contacts of Structural Units for 3OMO
  • Structure Factors (442 Kb)
  • Retrieve 3OMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OMO from S2C, [Save to disk]
  • Re-refined 3omo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OMO 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 3OMO
  • 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 3OMO, from MSDmotif at EBI
  • Fold representative 3omo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3omo_A] [3omo_C] [3omo] [3omo_B] [3omo_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3OMO: [HOLI ] by SMART
  • Other resources with information on 3OMO
  • Community annotation for 3OMO 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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