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Yorodumi- PDB-7q3f: Bromodomain-containing 4 BD1 in complex with the inhibitor CRCM5484 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q3f | ||||||
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Title | Bromodomain-containing 4 BD1 in complex with the inhibitor CRCM5484 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | PROTEIN BINDING / Epigenetic / Inhibition / Inhibitor / Selectivity / Complex / BDII | ||||||
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 / 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: 1.21 Å | ||||||
Authors | Carrasco, K. / Betzi, S. / Morelli, X. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: CRCM5484: A BET-BDII Selective Compound with Differential Anti-leukemic Drug Modulation Authors: Carrasco, K. / Montersino, C. / Derviaux, C. / Saez-Ayala, M. / Hoffer, L. / Restouin, A. / Castellano, R. / Casassa, J. / Roche, P. / Pasquier, E. / Combes, S. / Morelli, X. / Collette, Y. / Betzi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q3f.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q3f.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 7q3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q3f_validation.pdf.gz | 857.7 KB | Display | wwPDB validaton report |
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Full document | 7q3f_full_validation.pdf.gz | 858.5 KB | Display | |
Data in XML | 7q3f_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 7q3f_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/7q3f ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q3f | HTTPS FTP |
-Related structure data
Related structure data | 7q5oC 2ossS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15099.380 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-8M6 / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.3M NaNO3, 16% PEG3350, 5% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 28, 2020 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.21→48.72 Å / Num. obs: 39573 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.36 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 8.6 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.21→38.207 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.25 / Stereochemistry target values: ML
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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 max: 76.9 Å2 / Biso mean: 28.1729 Å2 / Biso min: 10.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.21→38.207 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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