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Open data
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Basic information
Entry | Database: PDB / ID: 6u4a | ||||||
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Title | BRD3-BD1 in complex with the cyclic peptide 3.1_3 | ||||||
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![]() | Transcription/Inhibitor / BET / bromodomain / macrocyclic peptide / BRD3 / inhibitor / RaPID / Transcription-Inhibitor complex | ||||||
Function / homology | ![]() lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patel, K. / Walshe, J.L. / Walport, L.J. / Mackay, J.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cyclic peptides can engage a single binding pocket through highly divergent modes. Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, ...Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Mackay, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.9 KB | Display | ![]() |
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Full document | ![]() | 456.1 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u61C ![]() 6u6kC ![]() 6u6lC ![]() 6u71C ![]() 6u72C ![]() 6u74C ![]() 6u8gC ![]() 6u8hC ![]() 6u8iC ![]() 6u8mC ![]() 6ulpC ![]() 6ulqC ![]() 6ultC ![]() 6ulvC ![]() 3s91S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15095.392 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1466.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #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: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium sulfate 0.1 M Bis-Tris propane 8.5 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→43.84 Å / Num. obs: 23076 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.88→1.92 Å / Num. unique obs: 1421 / CC1/2: 0.883 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3S91 Resolution: 1.88→43.82 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4008
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→43.82 Å
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Refine LS restraints |
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LS refinement shell |
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