+Open data
-Basic information
Entry | Database: PDB / ID: 7aqt | ||||||
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Title | NMR2 structure of BRD4-BD2 in complex with iBET-762 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | ONCOPROTEIN / BRD4 / BD2 / bromodomain / iBET-762 / NMR2 | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / NMR2 | ||||||
Authors | Orts, J. / Torres, F. / Milbradt, A.G. / Walser, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2022 Title: NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24. Authors: Torres, F. / Walser, R. / Kaderli, J. / Rossi, E. / Bobby, R. / Packer, M.J. / Sarda, S. / Walker, G. / Hitchin, J.R. / Milbradt, A.G. / Orts, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aqt.cif.gz | 411.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqt.ent.gz | 345.3 KB | Display | PDB format |
PDBx/mmJSON format | 7aqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqt_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 7aqt_full_validation.pdf.gz | 495.5 KB | Display | |
Data in XML | 7aqt_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 7aqt_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqt ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqt | HTTPS FTP |
-Related structure data
Related structure data | 7b9xC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12749.791 Da / Num. of mol.: 1 / Fragment: BRD4-BD2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-EAM / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 350 uM U-[12C,2H],U-15N,[13C,1H]-Ile-d1, [13C,1H]-Leu-d1/2, [13C,1H]-Val-g1/2 ILV-BRD4-BD2, 50 mM Na2HPO4, 500 uM [U-2H] TCEP, 420 uM iBET-762, 100 % [U-2H] D2O, 100% D2O Label: 15N_2H_1H-methyl-ILV / Solvent system: 100% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 mM / Label: sample_1 / pH: 6.7 pD / Pressure: 1 bar / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz |
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-Processing
NMR software | Name: CYANA / Developer: Guntert P. / Classification: refinement |
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Refinement | Method: NMR2 / Software ordinal: 1 |
NMR representative | Selection criteria: target function |
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 |