3OMP 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 0.198 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
70.720 70.720 109.810 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.05 Å
ligand W14 BindingDB enzyme
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] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (3omp.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (3omp.pdb2.gz) 83 Kb
  • Biological Unit Coordinates (3omp.pdb3.gz) 167 Kb
  • LPC: Ligand-Protein Contacts for 3OMP
  • CSU: Contacts of Structural Units for 3OMP
  • Structure Factors (559 Kb)
  • Retrieve 3OMP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OMP from S2C, [Save to disk]
  • Re-refined 3omp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OMP 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 3OMP
  • 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 3OMP, from MSDmotif at EBI
  • Fold representative 3omp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3omp_A] [3omp_B] [3omp_D] [3omp] [3omp_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3OMP: [HOLI ] by SMART
  • Alignments of the sequence of 3OMP with the sequences similar proteins can be viewed for 3OMP's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3OMP
  • Community annotation for 3OMP 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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