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- PDB-5o4s: Crystal structure of the human BRPF1 bromodomain in complex with BZ135 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o4s | ||||||
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Title | Crystal structure of the human BRPF1 bromodomain in complex with BZ135 | ||||||
![]() | Peregrin | ||||||
![]() | DNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription | ||||||
Function / homology | ![]() acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, J. / Caflisch, A. | ||||||
![]() | ![]() Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors. Authors: Zhu, J. / Zhou, C. / Caflisch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.1 KB | Display | ![]() |
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PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mwgC ![]() 5mwhC ![]() 5mwzC ![]() 5o4tC ![]() 5o55C ![]() 5o5aC ![]() 5o5fC ![]() 5o5hC ![]() 5ov8C ![]() 5owaC ![]() 6ekqC ![]() 4lc2S S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13703.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NO3 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-tris propane, pH6.5, 0.15 M Sodium Nitrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→38 Å / Num. obs: 29072 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.151 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1578 / CC1/2: 0.961 / % possible all: 99.4 |
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Processing
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Refinement | Starting model: 4LC2 Resolution: 1.75→38 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.0436 Å / Origin y: 4.6943 Å / Origin z: 8.7135 Å
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Refinement TLS group | Selection details: all |