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Yorodumi- PDB-7lay: Crystal structure of the first bromodomain (BD1) of human BRD3 bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lay | ||||||
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Title | Crystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179 | ||||||
Components | Bromodomain-containing protein 3 | ||||||
Keywords | GENE REGULATION/INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex | ||||||
Function / homology | Function and homology information lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Karim, M.R. / Bikowitz, M.J. / Schonbrunn, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lay.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lay.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/7lay ftp://data.pdbj.org/pub/pdb/validation_reports/la/7lay | HTTPS FTP |
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-Related structure data
Related structure data | 5v67C 5vboC 5vbpC 5vbqC 5vbrC 7bjyC 7k6gC 7k6hC 7ko0C 7l6dC 7l72C 7l73C 7l9gC 7l9jC 7l9kC 7l9lC 7lahC 7laiC 7lajC 7lakC 7lauC 7lazC 7lb4C 7lbtC 7lejC 7lekC 7lelC 7lemC 3nxbS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14586.843 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→100 Å / Num. obs: 49274 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.54 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.045 / Rrim(I) all: 0.107 / Χ2: 6.715 / Net I/σ(I): 20.5 / Num. measured all: 185069 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NXB Resolution: 1.45→42.729 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.64 / 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: 68.48 Å2 / Biso mean: 18.2637 Å2 / Biso min: 9.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→42.729 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 / Origin x: -23.6044 Å / Origin y: 7.0484 Å / Origin z: -13.0226 Å
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Refinement TLS group |
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