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Yorodumi- PDB-5hrx: Crystal structure of the fifth bromodomain of human PB1 in comple... -
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-Basic information
Entry | Database: PDB / ID: 5hrx | ||||||
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Title | Crystal structure of the fifth bromodomain of human PB1 in complex with 1-butylisochromeno[3,4-c]pyrazol-5(2H)-one) compound | ||||||
Components | Protein polybromo-1 | ||||||
Keywords | TRANSCRIPTION / PBRM1 / BRG1-associated factor 180 / chromatin remodeling | ||||||
Function / homology | Function and homology information regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Tallant, C. / Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Newman, J.A. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Mikros, E. / Knapp, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis. Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / ...Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / Savitsky, P. / Bagratuni, T. / Kastritis, E. / Terpos, E. / Filippakopoulos, P. / Muller, S. / Skaltsounis, A.L. / Downs, J.A. / Knapp, S. / Mikros, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hrx.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hrx.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/5hrx ftp://data.pdbj.org/pub/pdb/validation_reports/hr/5hrx | HTTPS FTP |
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-Related structure data
Related structure data | 5hrvC 5hrwC 5ii1C 5ii2C 5iidC 3g0jS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14648.000 Da / Num. of mol.: 2 / Fragment: UNP Residues 613-734 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.51 % / Description: Plate crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 30% PEG4K PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9207 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9207 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→29.21 Å / Num. all: 26823 / Num. obs: 26823 / % possible obs: 97.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.026 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 5 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.8 / % possible all: 96.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G0J Resolution: 1.73→29.21 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.419 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.679 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→29.21 Å
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Refine LS restraints |
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