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Open data
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Basic information
Entry | Database: PDB / ID: 5d3t | ||||||
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Title | First bromodomain of BRD4 bound to inhibitor XD47 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION / Gene regulation / Bromodomain / Inhibitor | ||||||
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 / chromatin / 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 | ![]() ![]() | ||||||
![]() | Wohlwend, D. / Huegle, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1). Authors: Hugle, M. / Lucas, X. / Weitzel, G. / Ostrovskyi, D. / Breit, B. / Gerhardt, S. / Einsle, O. / Gunther, S. / Wohlwend, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.8 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 737.1 KB | Display | ![]() |
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Full document | ![]() | 737.3 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d24C ![]() 5d25C ![]() 5d26C ![]() 5d3hC ![]() 5d3jC ![]() 5d3lC ![]() 5d3nC ![]() 5d3pC ![]() 5d3rC ![]() 5d3sC C: citing same article ( |
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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: 15099.380 Da / Num. of mol.: 1 / Fragment: First bromodomain, UNP residues 42-168 / Mutation: T43M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-56Y / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→13.2 Å / Num. obs: 12248 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.82→1.92 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1712 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.137 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→13.2 Å
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Refine LS restraints |
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