+Open data
-Basic information
Entry | Database: PDB / ID: 6hid | ||||||
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Title | The ATAD2 bromodomain in complex with compound 16 | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | CYTOSOLIC PROTEIN / Bromodomain / ATAD2 / inhibitor / complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.768 Å | ||||||
Authors | Sledz, P. / Caflisch, A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. Authors: Dolbois, A. / Batiste, L. / Wiedmer, L. / Dong, J. / Brutsch, M. / Huang, D. / Deerain, N.M. / Spiliotopoulos, D. / Cheng-Sanchez, I. / Laul, E. / Nevado, C. / Sledz, P. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hid.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hid.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 6hid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hid ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hid | HTTPS FTP |
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-Related structure data
Related structure data | 5f36SC 6epjC 6eptC 6epuC 6epvC 6epxC 6hi3C 6hi4C 6hi5C 6hi6C 6hi7C 6hi8C 6hiaC 6hibC 6hicC 6hieC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 15453.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999987 Å / Relative weight: 1 |
Reflection | Resolution: 1.768→39.916 Å / Num. obs: 47736 / % possible obs: 99 % / Redundancy: 6.09 % / CC1/2: 1 / Rrim(I) all: 0.046 / Net I/σ(I): 18.51 |
Reflection shell | Resolution: 1.77→1.88 Å / Redundancy: 2.99 % / Num. unique obs: 7333 / Rrim(I) all: 1.923 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5f36 Resolution: 1.768→39.916 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.768→39.916 Å
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Refine LS restraints |
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LS refinement shell |
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