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- PDB-7qyo: BAZ2A bromodomain in complex with acetylpyrrole derivative compound 79 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qyo | ||||||
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Title | BAZ2A bromodomain in complex with acetylpyrrole derivative compound 79 | ||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2A | ||||||
![]() | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | ![]() NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / DNA methylation-dependent heterochromatin formation / negative regulation of transcription by RNA polymerase I / lysine-acetylated histone binding / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / DNA methylation-dependent heterochromatin formation / negative regulation of transcription by RNA polymerase I / lysine-acetylated histone binding / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / chromatin remodeling / nuclear speck / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. Authors: Dalle Vedove, A. / Cazzanelli, G. / Batiste, L. / Marchand, J.R. / Spiliotopoulos, D. / Corsi, J. / D'Agostino, V.G. / Caflisch, A. / Lolli, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.2 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7b7bC ![]() 7b7gC ![]() 7b7iC ![]() 7b82C ![]() 7bc2C ![]() 7qvtC ![]() 7qvuC ![]() 7qvvC ![]() 7qwfC ![]() 7qwuC ![]() 7qwyC ![]() 7qx2C ![]() 7qx9C ![]() 7qxlC ![]() 7qyeC ![]() 7qytC ![]() 7qyuC ![]() 7qyvC ![]() 7qywC ![]() 7qz0C ![]() 7qz4C ![]() 7qzbC ![]() 7qzcC ![]() 7qziC ![]() 7qztC ![]() 7r01C ![]() 7r0bC ![]() 5mgjS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12492.001 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 1796-1899) Mutation: First two residues SM derive from the expression tag, double mutant E1845H/L1848S. Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.81 % / Mosaicity: 0.17 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9133 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 0.98→37.86 Å / Num. obs: 55493 / % possible obs: 99.4 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.015 / Rrim(I) all: 0.036 / Net I/σ(I): 25.1 / Num. measured all: 330609 / Scaling rejects: 123 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MGJ Resolution: 0.983→27.32 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.16 / Stereochemistry target values: ML
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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 max: 47.39 Å2 / Biso mean: 13.6862 Å2 / Biso min: 5.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.983→27.32 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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