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- PDB-7rn2: 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: 7rn2 | ||||||
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Title | Crystal structure of the first bromodomain of human BRD4 in complex with SJ001010551-2 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | CELL CYCLE / bromodomain-containing protein 4 isoform long / BRD4 / bromodomain containing protein 4 / mitotic chromosome associated 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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Stachowski, T.R. / Fischer, M. | ||||||
![]() | ![]() Title: From PROTAC to inhibitor: Structure-guided discovery of potent and orally bioavailable BET inhibitors. Authors: Koravovic, M. / Mayasundari, A. / Tasic, G. / Keramatnia, F. / Stachowski, T.R. / Cui, H. / Chai, S.C. / Jonchere, B. / Yang, L. / Li, Y. / Fu, X. / Hiltenbrand, R. / Paul, L. / Mishra, V. / ...Authors: Koravovic, M. / Mayasundari, A. / Tasic, G. / Keramatnia, F. / Stachowski, T.R. / Cui, H. / Chai, S.C. / Jonchere, B. / Yang, L. / Li, Y. / Fu, X. / Hiltenbrand, R. / Paul, L. / Mishra, V. / Klco, J.M. / Roussel, M.F. / Pomerantz, W.C. / Fischer, M. / Rankovic, Z. / Savic, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.9 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rmdC ![]() 3mxfS 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: 15099.380 Da / Num. of mol.: 1 / Fragment: first bromodomain (UNP residues 44-168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-5ZQ / |
#4: 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: 41.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris, pH 6.8, 20% PEG3350, 15% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→33.07 Å / Num. obs: 60488 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 14.17 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.05→1.07 Å / Num. unique obs: 2710 / CC1/2: 0.783 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3MXF Resolution: 1.05→33.07 Å / SU ML: 0.0835 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.33 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 18.76 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→33.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.07 Å
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Refinement TLS params. | Method: refined / Origin x: 29.8160219422 Å / Origin y: 25.3675188543 Å / Origin z: 9.03124259444 Å
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Refinement TLS group | Selection details: all |