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- PDB-7lro: Crystal structure of BPTF bromodomain in complex with inhibitor H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lro | |||||||||
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Title | Crystal structure of BPTF bromodomain in complex with inhibitor HZ-01-105 | |||||||||
![]() | Nucleosome-remodeling factor subunit BPTF | |||||||||
![]() | GENE REGULATION/INHIBITOR / BPTF / bromodomain / inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex | |||||||||
Function / homology | ![]() NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
Model details | Cocrystal structure of BPTF bromodomain | |||||||||
![]() | Chan, A. / Schonbrunn, E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. Authors: Zahid, H. / Buchholz, C.R. / Singh, M. / Ciccone, M.F. / Chan, A. / Nithianantham, S. / Shi, K. / Aihara, H. / Fischer, M. / Schonbrunn, E. / Dos Santos, C.O. / Landry, J.W. / Pomerantz, W.C.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.5 KB | Display | ![]() |
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PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 955.4 KB | Display | ![]() |
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Full document | ![]() | 956.9 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lp0C ![]() 7lpkC ![]() 7lrkC ![]() 7rwnC ![]() 7rwoC ![]() 7rwpC ![]() 7rwqC ![]() 7k6rS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 14455.415 Da / Num. of mol.: 2 / Fragment: BPTF bromodomain (uniprot residues 2917-3037) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-DMS / | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→33.1 Å / Num. obs: 43259 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.082 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3165 / CC1/2: 0.782 / Rrim(I) all: 0.586 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7K6R Resolution: 1.45→33.09 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.3 / 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: 51.81 Å2 / Biso mean: 13.647 Å2 / Biso min: 4.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→33.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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