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- PDB-8b5a: Human BRD3 bromodomain 2 in complex with a H4 peptide containing ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b5a | |||||||||
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Title | Human BRD3 bromodomain 2 in complex with a H4 peptide containing ApmTri (H4K20ApmTri) | |||||||||
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![]() | PEPTIDE BINDING PROTEIN / ApmTri / acetyl-lysine mimic / BET-Bromodomain / histone-peptide | |||||||||
Function / homology | ![]() lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Braun, M.B. / Bartlick, N. / Stehle, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family. Authors: Kirchgassner, S. / Braun, M.B. / Bartlick, N. / Koc, C. / Reinkemeier, C.D. / Lemke, E.A. / Stehle, T. / Schwarzer, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.3 KB | Display | ![]() |
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PDB format | ![]() | 48.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8b5bC ![]() 8b5cC ![]() 2oo1S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13032.073 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1269.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM potassium sodium tatrate 100 mM sodium citrate pH 5.6 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99989 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 14001 / % possible obs: 98.9 % / Redundancy: 25.2 % / Biso Wilson estimate: 41.79 Å2 / CC1/2: 1 / Net I/σ(I): 31.84 |
Reflection shell | Resolution: 1.92→1.97 Å / Num. unique obs: 1012 / CC1/2: 0.776 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OO1 Resolution: 1.92→36.73 Å / SU ML: 0.2888 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3417 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 48.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→36.73 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: -23.5585414241 Å / Origin y: -28.110201011 Å / Origin z: 3.23749531333 Å
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Refinement TLS group | Selection details: all |