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Yorodumi- PDB-7okd: Crystal structure of human BCL6 BTB domain in complex with compound 25 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7okd | ||||||
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Title | Crystal structure of human BCL6 BTB domain in complex with compound 25 | ||||||
Components | B-cell lymphoma 6 protein | ||||||
Keywords | TRANSCRIPTION / CANCER / LYMPHOMA / INHIBITOR | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Authors | Gunnell, E.A. / Le Bihan, Y.-V. / van Montfort, R.L.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket. Authors: Lloyd, M.G. / Huckvale, R. / Cheung, K.J. / Rodrigues, M.J. / Collie, G.W. / Pierrat, O.A. / Gatti Iou, M. / Carter, M. / Davis, O.A. / McAndrew, P.C. / Gunnell, E. / Le Bihan, Y.V. / ...Authors: Lloyd, M.G. / Huckvale, R. / Cheung, K.J. / Rodrigues, M.J. / Collie, G.W. / Pierrat, O.A. / Gatti Iou, M. / Carter, M. / Davis, O.A. / McAndrew, P.C. / Gunnell, E. / Le Bihan, Y.V. / Talbot, R. / Henley, A.T. / Johnson, L.D. / Hayes, A. / Bright, M.D. / Raynaud, F.I. / Meniconi, M. / Burke, R. / van Montfort, R.L.M. / Rossanese, O.W. / Bellenie, B.R. / Hoelder, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7okd.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7okd.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 7okd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7okd_validation.pdf.gz | 815.9 KB | Display | wwPDB validaton report |
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Full document | 7okd_full_validation.pdf.gz | 815.9 KB | Display | |
Data in XML | 7okd_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 7okd_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/7okd ftp://data.pdbj.org/pub/pdb/validation_reports/ok/7okd | HTTPS FTP |
-Related structure data
Related structure data | 7okeC 7okfC 7okgC 7okhC 7okiC 7okjC 7okkC 7oklC 7okmC 3bimS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16498.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Plasmid: pET48b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P41182 | ||||||
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#2: Chemical | ChemComp-VGW / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 1.5 microliter of BCL6-BTB at 10 mg/mL plus 1.5 microliter of a crystallisation solution consisting of 0.1 M Tris pH 7.5 and 0.80 M Na/K Tartrate, against 300 microliter of crystallisation solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 5, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→47.92 Å / Num. obs: 17565 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.099 / Net I/σ(I): 14.1 / Num. measured all: 224524 / Scaling rejects: 64 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BIM Resolution: 1.94→40.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.102
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Displacement parameters | Biso max: 132.2 Å2 / Biso mean: 47.68 Å2 / Biso min: 28.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→40.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 44
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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