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Open data
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Basic information
Entry | Database: PDB / ID: 7ugf | ||||||
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Title | First bromodomain of BRD4 liganded with BMS-536924 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION / bromodomain / small molecule ligand / complex | ||||||
Function / homology | ![]() RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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 | ![]() | 78.6 KB | Display | ![]() |
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PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ug5C ![]() 7ugeC ![]() 7ugiC ![]() 7uglC ![]() 8fupC ![]() 5kj0S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-N6I / ( | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.93 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350 |
-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: Nov 11, 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: 1.45→39.32 Å / Num. obs: 23514 / % possible obs: 98.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.45→1.49 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1512 / CC1/2: 0.952 / Rrim(I) all: 0.247 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KJ0 Resolution: 1.45→39.32 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.18 / 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: 74.52 Å2 / Biso mean: 19.414 Å2 / Biso min: 9.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→39.32 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 12.0952 Å / Origin y: 3.2729 Å / Origin z: 8.4863 Å
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Refinement TLS group |
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