2YEK Signaling Protein date Mar 25, 2011
title Crystal Structure Of The First Bromodomain Of Human Brd2 With The Inhibitor Gsk525762 (Ibet)
authors C.W.Chung
compound source
Molecule: Bromodomain-Containing Protein 2
Chain: A, B, C
Fragment: N-Terminal Bromodomain, Residues 67-200
Synonym: O27.1.1, Really Interesting New Gene 3 Protein, Hu
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.15546 R_Free 0.20079
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.243 55.639 66.231 90.00 93.63 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand EAM, SO4 BindingDB enzyme
Primary referenceDiscovery and Characterization of Small Molecule Inhibitors of the BET Family Bromodomains., Chung CW, Coste H, White JH, Mirguet O, Wilde J, Gosmini RL, Delves C, Magny SM, Woodward R, Hughes SA, Boursier EV, Flynn H, Bouillot AM, Bamborough P, Brusq JM, Gellibert FJ, Jones EJ, Riou AM, Homes P, Martin SL, Uings IJ, Toum J, Clement CA, Boullay AB, Grimley RL, Blandel FM, Prinjha RK, Lee K, Kirilovsky J, Nicodeme E, J Med Chem. 2011 Jun 9;54(11):3827-3838. Epub 2011 May 13. PMID:21568322
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (2yek.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (2yek.pdb2.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 2YEK
  • CSU: Contacts of Structural Units for 2YEK
  • Structure Factors (490 Kb)
  • Retrieve 2YEK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YEK from S2C, [Save to disk]
  • Re-refined 2yek structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YEK 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 2YEK
  • 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
  • 3D motif for 2YEK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yek] [2yek_C] [2yek_A] [2yek_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YEK: [BROMO ] by SMART
    • Other resources with information on 2YEK
  • Community annotation for 2YEK at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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