2YDW Nuclear Protein date Mar 24, 2011
title Crystal Structure Of The First Bromodomain Of Human Brd2 Wit Inhibitor Gw841819x
authors C.Chung, C.Delves, R.Woodward, O.Mirguet, E.Nicodeme
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_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.200 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.372 56.013 67.425 90.00 93.98 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand SO4, WSH 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] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (2ydw.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (2ydw.pdb2.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 2YDW
  • CSU: Contacts of Structural Units for 2YDW
  • Structure Factors (579 Kb)
  • Retrieve 2YDW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YDW from S2C, [Save to disk]
  • Re-refined 2ydw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YDW 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 2YDW
  • 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 2YDW, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ydw_A] [2ydw_C] [2ydw_B] [2ydw]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YDW: [BROMO ] by SMART
    • Other resources with information on 2YDW
  • Community annotation for 2YDW at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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