3LBZ Transcription date Jan 08, 2010
title Crystal Structure Of The Bcl6 Btb Domain Complexed With The Molecule Inhibitor 79-6
authors A.F.Ghetu, G.G.Prive
compound source
Molecule: B-Cell Lymphoma 6 Protein
Chain: A, B
Fragment: Btb Domain, Residues 5-129
Synonym: Bcl-6, Zinc Finger Protein 51, Laz-3 Protein, Bcl- Finger And Btb Domain-Containing Protein 27;
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bcl5, Bcl6, Laz3, Zbtb27, Znf51
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus (De3)
Expression_system_vector_type: Pet32
Expression_system_plasmid: Pet32a
symmetry Space Group: C 1 2 1
R_factor 0.213 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.712 38.611 78.817 90.00 114.70 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand Z88, Z89 enzyme
Primary referenceA small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo., Cerchietti LC, Ghetu AF, Zhu X, Da Silva GF, Zhong S, Matthews M, Bunting KL, Polo JM, Fares C, Arrowsmith CH, Yang SN, Garcia M, Coop A, Mackerell AD Jr, Prive GG, Melnick A, Cancer Cell. 2010 Apr 13;17(4):400-11. PMID:20385364
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (3lbz.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3LBZ
  • CSU: Contacts of Structural Units for 3LBZ
  • Structure Factors (187 Kb)
  • Retrieve 3LBZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LBZ from S2C, [Save to disk]
  • Re-refined 3lbz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3LBZ 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 3LBZ
  • 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 3LBZ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lbz] [3lbz_A] [3lbz_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LBZ: [BTB ] by SMART
    • Other resources with information on 3LBZ
  • Community annotation for 3LBZ 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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