+Open data
-Basic information
Entry | Database: PDB / ID: 7z9y | ||||||||||||
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Title | BRD4 in complex with FragLite2 | ||||||||||||
Components | Isoform C of Bromodomain-containing protein 4 | ||||||||||||
Keywords | TRANSCRIPTION / BRD4 / INHIBITOR / FRAGMENT / BROMODOMAIN / FRAGLITE | ||||||||||||
Function / homology | 4-IODOPYRAZOLE / Isoform C of Bromodomain-containing protein 4 Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||||||||
Authors | Turberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions. Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z9y.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z9y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z9y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7z9y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7z9y_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 7z9y_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/7z9y ftp://data.pdbj.org/pub/pdb/validation_reports/z9/7z9y | HTTPS FTP |
-Related structure data
Related structure data | 7ppxC 7qu7C 7qukC 7qumC 7qwoC 7qx1C 7qxtC 7qykC 7qylC 7qzmC 7qzyC 7qzzC 7r00C 7r05C 7r0yC 7z9hC 7z9iC 7z9jC 7z9nC 7z9oC 7z9sC 7z9uC 7z9wC 7za6C 7za7C 7za8C 7za9C 7zaaC 7zadC 7zaeC 7zajC 7zaqC 7zarC 7zatC 7ze6C 7ze7C 7zefC 7zenC 7zfnC 7zfoC 7zfsC 7zftC 7zfuC 7zfvC 7zfyC 7zfzC 7zg1C 7zg2C 5lrqS 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: 15294.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885-2 | ||||||
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#2: Chemical | #3: Chemical | #4: 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: 2.12 Å3/Da / Density % sol: 42.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.95397 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95397 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.04→39.69 Å / Num. obs: 59412 / % possible obs: 93.6 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.077 / Net I/σ(I): 9.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LRQ Resolution: 1.04→39.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.54 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.035 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.553 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→39.69 Å
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Refine LS restraints |
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LS refinement shell |
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