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Yorodumi- PDB-6zs4: Crystal structure of the fifth bromodomain of human protein polyb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zs4 | ||||||
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Title | Crystal structure of the fifth bromodomain of human protein polybromo-1 in complex with tert-butyl 4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazine-1-carboxylate | ||||||
Components | Protein polybromo-1 | ||||||
Keywords | GENE REGULATION / BROMODOMAIN / COMPLEX / SMALL MOLECULE / STRUCTURAL GENOMICS CONSORTIUM / SGC / TRANSCRIPTION | ||||||
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: 2 Å | ||||||
Authors | Preuss, F. / Joerger, A.C. / Kraemer, A. / Wanior, M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis. Authors: Wanior, M. / Preuss, F. / Ni, X. / Kramer, A. / Mathea, S. / Gobel, T. / Heidenreich, D. / Simonyi, S. / Kahnt, A.S. / Joerger, A.C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zs4.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zs4.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 6zs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zs4_validation.pdf.gz | 702.7 KB | Display | wwPDB validaton report |
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Full document | 6zs4_full_validation.pdf.gz | 703 KB | Display | |
Data in XML | 6zs4_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6zs4_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zs4 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zs4 | HTTPS FTP |
-Related structure data
Related structure data | 6zn6C 6znvC 6zs2C 6zs3C 5fh7S 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: 14648.000 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-QP8 / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 2.59 Å3/Da / Density % sol: 52.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% PEG 5000 MME, 0.2 M (NH4)2SO4, 0.1 M MES pH 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91842 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91842 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.4 Å / Num. obs: 9289 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 19.4431060534 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / Num. unique obs: 690 / CC1/2: 0.944 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FH7 Resolution: 2→36.4 Å / SU ML: 0.24561713279 / Cross valid method: FREE R-VALUE / σ(F): 1.3373977252 / Phase error: 26.3296095809 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: 28.2787160071 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.4 Å
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Refine LS restraints |
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LS refinement shell |
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