+Open data
-Basic information
Entry | Database: PDB / ID: 8cv6 | ||||||
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Title | Peptide 4.2B in complex with BRD4.2 | ||||||
Components |
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Keywords | TRANSCRIPTION / Cyclic Peptide Inhibitor Bromodomain | ||||||
Function / homology | Function and homology information Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Franck, C. / Mackay, J.P. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Structure / Year: 2023 Title: Discovery and characterization of cyclic peptides selective for the C-terminal bromodomains of BET family proteins. Authors: Franck, C. / Patel, K. / Walport, L.J. / Christie, M. / Norman, A. / Passioura, T. / Suga, H. / Payne, R.J. / Mackay, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cv6.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cv6.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 8cv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cv6_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 8cv6_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 8cv6_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 8cv6_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/8cv6 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/8cv6 | HTTPS FTP |
-Related structure data
Related structure data | 8cv4C 8cv5C 8cv7C 8dnqC 3uvvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14058.205 Da / Num. of mol.: 1 / Fragment: BD2 (UNP residues 347-464) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5BJ26 |
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#2: Protein/peptide | Mass: 2233.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-ACE / |
#4: Chemical | ChemComp-NH2 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 30% w/v PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953736 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953736 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.65 Å / Num. obs: 13420 / % possible obs: 97.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 1.02 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3 / Num. unique obs: 4431 / CC1/2: 0.851 / Rpim(I) all: 0.355 / Rrim(I) all: 0.67 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3UVV Resolution: 1.7→35.65 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1758 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: 19.23 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.65 Å
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Refine LS restraints |
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LS refinement shell |
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