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- PDB-5is4: Endothiapepsin in complex with chiral brominated primary amine fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5is4 | ||||||
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Title | Endothiapepsin in complex with chiral brominated primary amine fragment | ||||||
![]() | Endothiapepsin | ||||||
![]() | HYDROLASE / fragment screening / aspartic protease / inhibition | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Radeva, N. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic Fragment Screening of an Entire Library Authors: Radeva, N. / 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 | ![]() | 188.2 KB | Display | ![]() |
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PDB format | ![]() | 151.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 458.8 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ![]() 4y5lC ![]() 4y5mC ![]() 4y5nC ![]() 4y5pC ![]() 4yckC ![]() 4yctC ![]() 4ycyC ![]() 4yd3C ![]() 4yd4C ![]() 4yd5C ![]() 4yd6C ![]() 4yd7C ![]() 5dpzC ![]() 5dq1C ![]() 5dq2C ![]() 5dq4C ![]() 5dq5C ![]() 5dr0C ![]() 5dr1C ![]() 5dr3C ![]() 5dr4C ![]() 5dr7C ![]() 5dr8C ![]() 5hcoC ![]() 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, endothiapepsin |
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-Non-polymers , 6 types, 286 molecules ![](data/chem/img/6LY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-6LY / ( | ||||||
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#3: Chemical | ChemComp-PG4 / | ||||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.24 % |
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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: Jan 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→42.7 Å / Num. obs: 67872 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rsym value: 0.044 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.37→1.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PCW Resolution: 1.368→42.673 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.04 / 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: 1.368→42.673 Å
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Refine LS restraints |
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LS refinement shell |
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