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- PDB-8tnd: De novo designed protein binds poly ADP ribose polymerase inhibit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tnd | ||||||
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Title | De novo designed protein binds poly ADP ribose polymerase inhibitors (PARPi) - holo veliparib | ||||||
![]() | De novo designed protein | ||||||
![]() | DE NOVO PROTEIN / drug binding / 4-helix bundle / de novo design / PARPi / veliparib | ||||||
Function / homology | Chem-78P![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, L. / DeGrado, W.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: De novo design of drug-binding proteins with predictable binding energy and specificity. Authors: Lu, L. / Gou, X. / Tan, S.K. / Mann, S.I. / Yang, H. / Zhong, X. / Gazgalis, D. / Valdiviezo, J. / Jo, H. / Wu, Y. / Diolaiti, M.E. / Ashworth, A. / Polizzi, N.F. / DeGrado, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8tn1C ![]() 8tn6C ![]() 8tnbC ![]() 8tncC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16203.947 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→202.35 Å / Num. obs: 123927 / % possible obs: 99.4 % / Redundancy: 67.6 % / Biso Wilson estimate: 18.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.011 / Χ2: 0.87 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.29→1.31 Å / Num. unique obs: 5369 / CC1/2: 0.363 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→78.59 Å
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Refine LS restraints |
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LS refinement shell |
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