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Open data
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Basic information
Entry | Database: PDB / ID: 4y5l | ||||||
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Title | Endothiapepsin in its apo form | ||||||
![]() | Endothiapepsin![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schiebel, J. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic Fragment Screening of an Entire Library Authors: Schiebel, J. / Heine, A. / Klebe, G. #1: ![]() Title: A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes. Authors: Koester, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.2 KB | Display | ![]() |
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PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4y35C ![]() 4y36C ![]() 4y37C ![]() 4y39C ![]() 4y3eC ![]() 4y3fC ![]() 4y3gC ![]() 4y3mC ![]() 4y3nC ![]() 4y3pC ![]() 4y3qC ![]() 4y3rC ![]() 4y3sC ![]() 4y3wC ![]() 4y3xC ![]() 4y3zC ![]() 4y41C ![]() 4y43C ![]() 4y44C ![]() 4y45C ![]() 4y47C ![]() 4y4aC ![]() 4y4bC ![]() 4y4eC ![]() 4y4tC ![]() 4y4uC ![]() 4y4wC ![]() 4y4xC ![]() 4y4zC ![]() 4y50C ![]() 4y51C ![]() 4y53C ![]() 4y54C ![]() 4y56C ![]() 4y57C ![]() 4y5mC ![]() 4y5nC ![]() 4y5pC ![]() 4yckC ![]() 4yctC ![]() 4ycyC ![]() 4yd3C ![]() 4yd4C ![]() 4yd5C ![]() 4yd6C ![]() 4yd7C ![]() 5dpzC ![]() 5dq1C ![]() 5dq2C ![]() 5dq4C ![]() 5dq5C ![]() 5dr0C ![]() 5dr1C ![]() 5dr3C ![]() 5dr4C ![]() 5dr7C ![]() 5dr8C ![]() 5hcoC ![]() 5is4C ![]() 5isjC ![]() 5iskC ![]() 5j25C ![]() 3pcwS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P11838, ![]() |
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-Non-polymers , 7 types, 343 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-PGE / | ![]() #5: Chemical | ChemComp-PG4 / | ![]() #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-PEG / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.65 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000, crystals obtained by streak-seeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.99→42.73 Å / Num. obs: 177093 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.038 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 0.99→1.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.501 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3PCW Resolution: 0.99→42.727 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 10.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→42.727 Å
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Refine LS restraints |
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LS refinement shell |
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