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Open data
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Basic information
Entry | Database: PDB / ID: 7zfs | ||||||||||||
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Title | BRD4 in complex with FragLite32 | ||||||||||||
![]() | Bromodomain-containing protein 4 | ||||||||||||
![]() | TRANSCRIPTION / FragLites / anomalous / BRD4 / Fragment screening | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Turberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions. Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 864.6 KB | Display | ![]() |
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Full document | ![]() | 864.7 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ppxC ![]() 7qu7C ![]() 7qukC ![]() 7qumC ![]() 7qwoC ![]() 7qx1C ![]() 7qxtC ![]() 7qykC ![]() 7qylC ![]() 7qzmC ![]() 7qzyC ![]() 7qzzC ![]() 7r00C ![]() 7r05C ![]() 7r0yC ![]() 7z9hC ![]() 7z9iC ![]() 7z9jC ![]() 7z9nC ![]() 7z9oC ![]() 7z9sC ![]() 7z9uC ![]() 7z9wC ![]() 7z9yC ![]() 7za6C ![]() 7za7C ![]() 7za8C ![]() 7za9C ![]() 7zaaC ![]() 7zadC ![]() 7zaeC ![]() 7zajC ![]() 7zaqC ![]() 7zarC ![]() 7zatC ![]() 7ze6C ![]() 7ze7C ![]() 7zefC ![]() 7zenC ![]() 7zfnC ![]() 7zfoC ![]() 7zftC ![]() 7zfuC ![]() 7zfvC ![]() 7zfyC ![]() 7zfzC ![]() 7zg1C ![]() 7zg2C ![]() 5lrqS 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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Unit cell |
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Components
#1: Protein | Mass: 15294.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-IS0 / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.911635 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.25→39.49 Å / Num. obs: 36606 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.043 / Rrim(I) all: 0.116 / Net I/σ(I): 10.6 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LRQ Resolution: 1.25→39.49 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.16 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.055 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.235 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→39.49 Å
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Refine LS restraints |
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LS refinement shell |
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