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Yorodumi- PDB-4hxn: Brd4 Bromodomain 1 complex with 4-(2-FLUOROPHENYL)-1,3-THIAZOL-2(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hxn | ||||||
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Title | Brd4 Bromodomain 1 complex with 4-(2-FLUOROPHENYL)-1,3-THIAZOL-2(3H)-ONE inhibitor | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | PROTEIN BINDING/INHIBITOR / BRD4 / Bromodomain / four alpha helices / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / 4-(2-fluorophenyl)-1,3-thiazol-2(3H)-one / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å | ||||||
Authors | Chen, T.T. / Cao, D.Y. / Chen, W.Y. / Xiong, B. / Shen, J.K. / Xu, Y.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Fragment-Based Drug Discovery of 2-Thiazolidinones as Inhibitors of the Histone Reader BRD4 Bromodomain. Authors: Zhao, L. / Cao, D. / Chen, T. / Wang, Y. / Miao, Z. / Xu, Y. / Chen, W. / Wang, X. / Li, Y. / Du, Z. / Xiong, B. / Li, J. / Xu, C. / Zhang, N. / He, J. / Shen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hxn.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hxn.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hxn_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 4hxn_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 4hxn_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4hxn_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/4hxn ftp://data.pdbj.org/pub/pdb/validation_reports/hx/4hxn | HTTPS FTP |
-Related structure data
Related structure data | 4hxkC 4hxlC 4hxmC 4hxoC 4hxpC 4hxrC 4hxsC 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: 14883.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: O60885 |
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#2: Chemical | ChemComp-1A7 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.49→40.497 Å / Num. obs: 37588 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.726 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.56 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→40.497 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8703 / SU ML: 0.13 / σ(F): 1.48 / Phase error: 19.9 / 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: 46.21 Å2 / Biso mean: 15.3306 Å2 / Biso min: 5.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→40.497 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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