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Open data
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Basic information
Entry | Database: PDB / ID: 7ug5 | ||||||
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Title | Second bromodomain of BRD3 liganded with BMS-536924 | ||||||
![]() | Bromodomain-containing protein 3 | ||||||
![]() | TRANSCRIPTION / bromodomain / small molecule ligand / complex | ||||||
Function / homology | ![]() lncRNA binding / endodermal cell differentiation / protein localization to chromatin / lysine-acetylated histone binding / molecular condensate scaffold activity / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schonbrunn, E. / Bikowitz, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis of CBP and EP300 interaction with kinase inhibitors Authors: Schonbrunn, E. / Bikowitz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.8 KB | Display | ![]() |
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PDB format | ![]() | 92.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ugeC ![]() 7ugfC ![]() 7ugiC ![]() 7uglC ![]() 8fupC ![]() 7l9lS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13089.126 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 30% v/v Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.8 Å / Num. obs: 56001 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.9 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.121 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.8→1.85 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4129 / CC1/2: 0.677 / Rrim(I) all: 0.887 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7L9L Resolution: 1.8→19.8 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.21 / 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: 80.22 Å2 / Biso mean: 26.0203 Å2 / Biso min: 11.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→19.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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