+Open data
-Basic information
Entry | Database: PDB / ID: 6zn6 | ||||||
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Title | Protein polybromo-1 (PB1 BD2) Bound To MW278 | ||||||
Components | Protein polybromo-1 | ||||||
Keywords | PROTEIN BINDING / Bromodomain Inhibitor Epigenetics | ||||||
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 / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / 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: 2.02 Å | ||||||
Authors | Preuss, F. / Mathea, S. / Chatterjee, D. / Wanior, M. / Joerger, A.C. / Knapp, S. | ||||||
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 | 6zn6.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zn6.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zn6_validation.pdf.gz | 927.1 KB | Display | wwPDB validaton report |
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Full document | 6zn6_full_validation.pdf.gz | 926.6 KB | Display | |
Data in XML | 6zn6_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 6zn6_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/6zn6 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/6zn6 | HTTPS FTP |
-Related structure data
Related structure data | 6znvC 6zs2C 6zs3C 6zs4C 3hmfS 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: 13231.299 Da / Num. of mol.: 2 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 | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M NaCl 25% (w/v) PEG3350 0.1 M bis-tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→36.6 Å / Num. obs: 18158 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.02→2.09 Å / Num. unique obs: 1777 / CC1/2: 0.777 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HMF Resolution: 2.02→36.6 Å / SU ML: 0.3811 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 31.2598 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: 24.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→36.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.4609437206 Å / Origin y: 13.4159787053 Å / Origin z: 13.089626006 Å
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Refinement TLS group |
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