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- PDB-7lwf: Crystal structure of the BCL6 BTB domain in complex with OICR-9320 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lwf | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with OICR-9320 | ||||||
![]() | B-cell lymphoma 6 protein | ||||||
![]() | TRANSCRIPTION/INHIBITOR / immunity / inflammatory response / transcription repressor / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | ![]() regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation ...regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / cell morphogenesis / protein localization / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuntz, D.A. / Prive, G.G. | ||||||
![]() | ![]() Title: Discovery of OICR12694: A Novel, Potent, Selective, and Orally Bioavailable BCL6 BTB Inhibitor. Authors: Mamai, A. / Chau, A.M. / Wilson, B.J. / Watson, I.D. / Joseph, B.B. / Subramanian, P.R. / Morshed, M.M. / Morin, J.A. / Prakesch, M.A. / Lu, T. / Connolly, P. / Kuntz, D.A. / Pomroy, N.C. / ...Authors: Mamai, A. / Chau, A.M. / Wilson, B.J. / Watson, I.D. / Joseph, B.B. / Subramanian, P.R. / Morshed, M.M. / Morin, J.A. / Prakesch, M.A. / Lu, T. / Connolly, P. / Kuntz, D.A. / Pomroy, N.C. / Poda, G. / Nguyen, K. / Marcellus, R. / Strathdee, G. / Theriault, B. / Subramaniam, R. / Mohammed, M. / Abibi, A. / Chan, M. / Winston, J. / Kiyota, T. / Undzys, E. / Aman, A. / Austin, N. / Du Jardin, M. / Packman, K. / Phillippar, U. / Attar, R. / Edwards, J. / O'Meara, J. / Uehling, D.E. / Al-Awar, R. / Prive, G.G. / Isaac, M.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.6 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 716.8 KB | Display | ![]() |
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Full document | ![]() | 718.2 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lweC ![]() 7lwgC ![]() 7lzqC ![]() 7lzsC ![]() 3lbzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14415.693 Da / Num. of mol.: 1 / Fragment: BTB domain, residues 5-129 / Mutation: C8Q, C67R, C84N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P41182 |
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#2: Chemical | ChemComp-YNA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG, citrate cocrystallization, crystal soaked with Hepes pH 7.4, 20% glycerol, ligand prior to freezing. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→36.21 Å / Num. obs: 34189 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.77 Å2 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.022 / Rrim(I) all: 0.032 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.22→1.224 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 336 / Rpim(I) all: 0.303 / Rrim(I) all: 0.456 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LBZ Resolution: 1.22→29.96 Å / SU ML: 0.1183 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.062 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→29.96 Å
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Refine LS restraints |
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LS refinement shell |
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