+Open data
-Basic information
Entry | Database: PDB / ID: 6epx | ||||||
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Title | The ATAD2 bromodomain in complex with compound 3 | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | CYTOSOLIC PROTEIN / Bromodomain / ATAD2 / inhibitor / complex | ||||||
Function / homology | Function and homology information nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 | 6epx.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6epx.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 6epx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/6epx ftp://data.pdbj.org/pub/pdb/validation_reports/ep/6epx | HTTPS FTP |
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-Related structure data
Related structure data | 5f36C 6epjC 6eptC 6epuC 6epvC 6hi3C 6hi4C 6hi5C 6hi6C 6hi7C 6hi8C 6hiaC 6hibC 6hicC 6hidC 6hieC 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) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #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: 4.09 Å3/Da / Density % sol: 69.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2M ammonium sulfate, 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: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.79 Å / Num. obs: 42520 / % possible obs: 99.7 % / Redundancy: 4.33 % / CC1/2: 1 / Rrim(I) all: 0.035 / Net I/σ(I): 23.05 |
Reflection shell | Resolution: 1.84→1.95 Å / Redundancy: 2.64 % / Mean I/σ(I) obs: 1.64 / Num. unique obs: 6773 / CC1/2: 0.697 / Rrim(I) all: 0.651 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→48.79 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→48.79 Å
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Refine LS restraints |
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LS refinement shell |
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