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- PDB-5l97: Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l97 | |||||||||
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Title | Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 3 | |||||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2B | |||||||||
![]() | TRANSCRIPTION / four helical bundle | |||||||||
Function / homology | ![]() chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Lolli, G. / Marchand, J.-R. / Caflisch, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation. Authors: Marchand, J.R. / Lolli, G. / Caflisch, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
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PDB format | ![]() | 45.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.2 KB | Display | ![]() |
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Full document | ![]() | 810.4 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l8tC ![]() 5l8uC ![]() 5l96C ![]() 5l98C ![]() 5l99C ![]() 4ir5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 13531.574 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Mutation: First two residues SM derive from the expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-6RW / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.8 % / Mosaicity: 0.31 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG500MME (20%), PEG1000 (2%), PEG3350 (2%), PEG20000 (10%), MPD (2%) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.05→48.36 Å / Num. obs: 14688 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 30.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 14.1 / Num. measured all: 93132 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IR5 Resolution: 2.05→48.358 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.01 Å2 / Biso mean: 51.13 Å2 / Biso min: 26.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→48.358 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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