3OMQ	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 0.205 R_Free 0.260
crystal cell	length a length b length c angle alpha angle beta angle gamma 70.590 70.590 110.090 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.97 Å
ligand	W23 BindingDB	enzyme
Primary reference	Design 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 (3omq.pdb1.gz) 86 Kb Biological Unit Coordinates (3omq.pdb2.gz) 83 Kb Biological Unit Coordinates (3omq.pdb3.gz) 167 Kb LPC: Ligand-Protein Contacts for 3OMQ CSU: Contacts of Structural Units for 3OMQ Structure Factors (629 Kb) Retrieve 3OMQ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3OMQ from S2C, [Save to disk] Re-refined 3omq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3OMQ 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3OMQ

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 3OMQ, from MSDmotif at EBI Fold representative 3omq from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3omq_A] [3omq_B] [3omq_C] [3omq_D] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3OMQ with the sequences similar proteins can be viewed for 3OMQ'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 3OMQ

Community annotation for 3OMQ 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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