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Yorodumi- PDB-5x4p: Crystal structure of the BCL6 BTB domain in complex with Compound 6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x4p | ||||||
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Title | Crystal structure of the BCL6 BTB domain in complex with Compound 6 | ||||||
Components | B-cell lymphoma 6 protein | ||||||
Keywords | Transcription/Inhibitor / Transcription Repressor / Transcription-Inhibitor complex | ||||||
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 / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / FOXO-mediated transcription of cell death genes / negative regulation of Rho protein signal transduction / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / 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 / heterochromatin formation / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / protein localization / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / Resolution: 2.06 Å | ||||||
Authors | Sogabe, S. / Ida, K. / Lane, W. / Snell, G. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach Authors: Kamada, Y. / Sakai, N. / Sogabe, S. / Ida, K. / Oki, H. / Sakamoto, K. / Lane, W. / Snell, G. / Iida, M. / Imaeda, Y. / Sakamoto, J. / Matsui, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x4p.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x4p.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 5x4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x4p_validation.pdf.gz | 719.3 KB | Display | wwPDB validaton report |
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Full document | 5x4p_full_validation.pdf.gz | 719.6 KB | Display | |
Data in XML | 5x4p_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 5x4p_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/5x4p ftp://data.pdbj.org/pub/pdb/validation_reports/x4/5x4p | HTTPS FTP |
-Related structure data
Related structure data | 5x4mC 5x4nC 5x4oC 5x4qC 1r28S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16287.733 Da / Num. of mol.: 1 / Fragment: UNP residues 5-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182 |
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#2: Chemical | ChemComp-7ZO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris, potassium/sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 13032 / % possible obs: 97.5 % / Redundancy: 11.5 % / Rsym value: 0.069 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.06→2.1 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.3 / Rsym value: 1 / % possible all: 86 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R28 Resolution: 2.06→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.735 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.591 Å2
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Refinement step | Cycle: 1 / Resolution: 2.06→40 Å
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Refine LS restraints |
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