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Yorodumi- PDB-6v0q: Crystal structure of the bromodomain of human BRD7 bound to TG003 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v0q | ||||||
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Title | Crystal structure of the bromodomain of human BRD7 bound to TG003 | ||||||
Components | Bromodomain-containing protein 7 | ||||||
Keywords | GENE REGULATION / BRD7 / BAF / PBAF / mSWI/SNF / TG003 | ||||||
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 / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / regulation of mitotic cell cycle / positive regulation of cell differentiation / lysine-acetylated histone binding / kinetochore / Wnt signaling pathway / nuclear matrix / transcription corepressor activity / p53 binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / cell cycle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Model details | APO | ||||||
Authors | Karim, M.R. / Chan, A. / Schonbrunn, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains. Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v0q.cif.gz | 227.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v0q.ent.gz | 175.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v0q_validation.pdf.gz | 300.1 KB | Display | wwPDB validaton report |
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Full document | 6v0q_full_validation.pdf.gz | 304.2 KB | Display | |
Data in XML | 6v0q_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 6v0q_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/6v0q ftp://data.pdbj.org/pub/pdb/validation_reports/v0/6v0q | HTTPS FTP |
-Related structure data
Related structure data | 6ppaSC 6uzfC 6v0sC 6v0uC 6v0xC 6v14C 6v16C 6v17C 6v1bC 6v1eC 6v1fC 6v1hC 6v1kC 6v1lC 6v1uC 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14394.644 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD7, BP75, CELTIX1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q9NPI1 |
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-Non-polymers , 6 types, 498 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-EAE / ( #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M (NH4)2SO4, 0.05 M Bis-tris (pH 6.5), and 30 % Pentaerythritol ethoxylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→37.68 Å / Num. obs: 56788 / % possible obs: 98.5 % / Redundancy: 6.728 % / Biso Wilson estimate: 27.298 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.035 / Net I/σ(I): 19.77 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PPA Resolution: 1.69→37.68 Å / SU ML: 0.1675 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.3428
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→37.68 Å
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Refine LS restraints |
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LS refinement shell |
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