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Yorodumi- PDB-6kek: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6-h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kek | ||||||
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Title | Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6-hydroxy-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / BRD4 / bromodomain 1 | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.553 Å | ||||||
Authors | Lee, B.I. / Park, T.H. | ||||||
Funding support | Korea, Democratic People's Republic Of, 1items
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Citation | Journal: Molecules / Year: 2021 Title: Synthesis and Structure-Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research. Authors: Yoo, M. / Park, T.H. / Yoo, M. / Kim, Y. / Lee, J.Y. / Lee, K.M. / Ryu, S.E. / Lee, B.I. / Jung, K.Y. / Park, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kek.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kek.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kek_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6kek_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6kek_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 6kek_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6kek ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6kek | HTTPS FTP |
-Related structure data
Related structure data | 6kecC 6kehC 6keiC 6kejC 2ossS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15025.235 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 | ||||||
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#2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-D7L / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.73 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 6 M sodium formate, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 18038 / % possible obs: 98.4 % / Redundancy: 5.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.054 / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 0.557 / Num. unique obs: 835 / CC1/2: 0.839 / Rpim(I) all: 0.282 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.553→39.71 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.46 Å2 / Biso mean: 16.0969 Å2 / Biso min: 6.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.553→39.71 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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