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- PDB-4ty9: An Ligand-observed Mass Spectrometry-based Approach Integrated in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ty9 | ||||||
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Title | An Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline | ||||||
![]() | Polyprotein![]() | ||||||
![]() | TRANAFERASE/TRANSFERASE INHIBITOR / ![]() | ||||||
Function / homology | ![]() serine-type peptidase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Shui, W. / Yang, C. / Lin, J. / Chen, X. / Qin, S. / Chen, S. | ||||||
![]() | ![]() Title: A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline Authors: Chen, X. / Qin, S. / Chen, S. / Li, J. / Li, L. / Wang, Z. / Wang, Q. / Lin, J. / Yang, C. / Shui, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410.7 KB | Display | ![]() |
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PDB format | ![]() | 337.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4txsC ![]() 4ty8C ![]() 4tyaC ![]() 4tybC ![]() 4txf C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 62766.992 Da / Num. of mol.: 4 / Mutation: I539L, G549S, W550M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-3B0 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: PEG4000, Dithiothreitol, 2-(N-morpholino)ethanesulfonic acid, Glycerin PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 25, 2013 |
Radiation | Monochromator: Cu filter / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.78→50 Å / Num. obs: 66538 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 12.5 |
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Processing
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Refinement | Resolution: 2.78→42.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 15.728 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.51 Å2
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Refinement step | Cycle: final / Resolution: 2.78→42.79 Å
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Refine LS restraints |
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