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Open data
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Basic information
Entry | Database: PDB / ID: 5o3d | ||||||||||||
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Title | Human Brd2(BD2) mutant in complex with 9-ET | ||||||||||||
![]() | Bromodomain-containing protein 2 | ||||||||||||
![]() | TRANSCRIPTION / The Bromodomain and Extra-Terminal Domain (BET) Family Chromatin binding protein | ||||||||||||
Function / homology | ![]() acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Chan, K.-H. / Runcie, A.C. / Ciulli, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition. Authors: Runcie, A.C. / Zengerle, M. / Chan, K.H. / Testa, A. / van Beurden, L. / Baud, M.G.J. / Epemolu, O. / Ellis, L.C.J. / Read, K.D. / Coulthard, V. / Brien, A. / Ciulli, 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 | ![]() | 45.9 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5o38C ![]() 5o39C ![]() 5o3aC ![]() 5o3bC ![]() 5o3cC ![]() 5o3eC ![]() 5o3fC ![]() 5o3gC ![]() 5o3hC ![]() 5o3iC ![]() 4qeuS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13361.383 Da / Num. of mol.: 1 / Mutation: L383V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-9J5 / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-DQW / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.25 Details: 0.1M Tris pH8.25 55% Pentaerythritol propoxylate (5/4 PO/OH) 0.2M Imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→32.003 Å / Num. obs: 16364 / % possible obs: 98.83 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05236 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.07519 / Num. unique obs: 1536 / CC1/2: 0.994 / % possible all: 94.76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QEU Resolution: 1.6→32.003 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.2 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→32.003 Å
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Refine LS restraints |
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LS refinement shell |
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