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- PDB-5i40: BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i40 | ||||||
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Title | BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one) | ||||||
![]() | Bromodomain-containing protein 9 | ||||||
![]() | RNA BINDING PROTEIN / Bromodomain Inhibitor Epigenetics Structure-based drug design | ||||||
Function / homology | ![]() GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murray, J.M. | ||||||
![]() | ![]() Title: Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / ...Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / Hewitt, M.C. / Huang, H.R. / Jayaram, H. / Kiefer, J.R. / Jiang, Y. / Murray, J. / Nasveschuk, C.G. / Pardo, E. / Poy, F. / Romero, F.A. / Tang, Y. / Wang, J. / Xu, Z. / Zawadzke, L.E. / Zhu, X. / Albrecht, B.K. / Magnuson, S.R. / Bellon, S. / Cochran, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
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Full document | ![]() | 452.1 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i1qC ![]() 5i29C ![]() 5i7xC ![]() 5i7yC ![]() 5i80C ![]() 5i88C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11856.921 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-67N / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 277.1 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M sodium formate 10-15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 173 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.04→50 Å / Num. obs: 49565 / % possible obs: 91.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.029 / Rrim(I) all: 0.051 / Χ2: 1.334 / Net I/av σ(I): 29.167 / Net I/σ(I): 10.5 / Num. measured all: 145238 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.26 Å2 / Biso mean: 15.6803 Å2 / Biso min: 7.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.0402→23.12 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: 18
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