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Open data
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Basic information
Entry | Database: PDB / ID: 7z9i | ||||||||||||
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Title | ATAD2 in complex with PepLite-Ala | ||||||||||||
![]() | ATPase family AAA domain-containing protein 2 | ||||||||||||
![]() | TRANSCRIPTION / ATAD2 / INHIBITOR / FRAGMENT / BROMODOMAIN / FRAGLITE | ||||||||||||
Function / homology | ![]() 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 | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Turberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 683.3 KB | Display | ![]() |
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Full document | ![]() | 684.5 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ppxC ![]() 7qu7C ![]() 7qukC ![]() 7qumC ![]() 7qwoC ![]() 7qx1C ![]() 7qxtC ![]() 7qykC ![]() 7qylC ![]() 7qzmC ![]() 7qzyC ![]() 7qzzC ![]() 7r00C ![]() 7r05C ![]() 7r0yC ![]() 7z9hC ![]() 7z9jC ![]() 7z9nC ![]() 7z9oC ![]() 7z9sC ![]() 7z9uC ![]() 7z9wC ![]() 7z9yC ![]() 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 ![]() 3daiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 207 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IJR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IJR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-IJR / ( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate / PH range: 6-7 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.5→61.54 Å / Num. obs: 41568 / % possible obs: 99.5 % / Redundancy: 20.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Rrim(I) all: 0.118 / Net I/σ(I): 11.9 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 16.8 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DAI Resolution: 1.5→48.702 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.453 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.062 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: 34.712 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→48.702 Å
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Refine LS restraints |
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LS refinement shell |
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