3BQD Protein Binding date Dec 20, 2007
title Doubling The Size Of The Glucocorticoid Receptor Ligand Binding Pocket By Deacylcortivazol
authors H.E.Xu
compound source
Molecule: Glucocorticoid Receptor
Chain: A
Fragment: Glucocorticoid Receptor Ligand Binding Domain (Residues 525-777);
Synonym: Gr, Nuclear Receptor Subfamily 3 Group C Member 1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr3c1, Grl
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24

Molecule: Nuclear Receptor Coactivator 1
Chain: B
Fragment: Nuclear Receptor Coactivator 1 Isoform 1 Coactivator Motif (Residues 739-751);
Synonym: Ncoa-1, Steroid Receptor Coactivator 1, Src-1, Rip160, Protein Hin-2, Renal Carcinoma Antigen Ny-Ren-52;
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Derived From Gene Sequence
symmetry Space Group: P 62
R_factor 0.231 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
93.800 93.800 130.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand DAY enzyme Transferase E.C. BRENDA
Primary referenceDoubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol., Suino-Powell K, Xu Y, Zhang C, Tao YG, Tolbert WD, Simons SS Jr, Xu HE, Mol Cell Biol. 2007 Dec 26;. PMID:18160712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (3bqd.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 3BQD
  • CSU: Contacts of Structural Units for 3BQD
  • Likely Quarternary Molecular Structure file(s) for 3BQD
  • Structure Factors (144 Kb)
  • Retrieve 3BQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BQD from S2C, [Save to disk]
  • Re-refined 3bqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BQD 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 3BQD
  • 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 3BQD, from MSDmotif at EBI
  • Fold representative 3bqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bqd_B] [3bqd_A] [3bqd]
  • SWISS-PROT database: [P04150] [Q15788]
  • Domain organization of [GCR_HUMAN] [NCOA1_HUMAN] by SWISSPFAM
  • Domain found in 3BQD: [HOLI ] by SMART
  • Other resources with information on 3BQD
  • Community annotation for 3BQD 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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