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- PDB-6lg4: crystal structure of the first bromodomain of human BRD4 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lg4 | ||||||
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Title | crystal structure of the first bromodomain of human BRD4 in complex with compound BDF-1024 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION / BRD4 / Inhibitor / Complex / DNA BINDING PROTEIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Xu, H. / Zuo, Y. / Zhang, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Lead-Opt: An efficient tool for structural optimization of lead compounds Authors: Xu, H. / Zuo, Y. / Zhang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.3 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.2 KB | Display | ![]() |
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Full document | ![]() | 773.2 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lg5C ![]() 6lg6C ![]() 6lg7C ![]() 6lg8C ![]() 6lg9C ![]() 5z5tS S: Starting model for refinement 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14883.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EC0 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 10-15% glycerol, 4M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→39.23 Å / Num. obs: 10897 / % possible obs: 96.83 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.36 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.158 / Net I/σ(I): 17.66 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.5759 / Num. unique obs: 1073 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Z5T Resolution: 1.85→39.23 Å / SU ML: 0.1945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0621
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.93 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.23 Å
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Refine LS restraints |
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LS refinement shell |
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