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Open data
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Basic information
Entry | Database: PDB / ID: 4y3a | ||||||
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Title | Endothiapepsin in complex with fragment 181 | ||||||
![]() | Endothiapepsin | ||||||
![]() | HYDROLASE / fragment screening / aspartic protease / inhibition | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ehrmann, F.R. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic Fragment Sreening of an Entire Library Authors: Ehrmann, F.R. / 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 | ![]() | 201.7 KB | Display | ![]() |
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PDB format | ![]() | 164.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 753 KB | Display | ![]() |
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Full document | ![]() | 753.1 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y3hC ![]() 4y3lC ![]() 4y3tC ![]() 4y58C ![]() 4y5aC ![]() 4y5bC ![]() 4y5cC ![]() 4y5eC ![]() 4y5gC ![]() 4y5kC ![]() 3pcwS S: Starting model for refinement 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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1 |
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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, 323 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/45O.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/45O.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-45O / | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.98 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1M 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: Apr 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→42.68 Å / Num. obs: 102974 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.032 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.17→1.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.3 / % possible all: 72.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PCW Resolution: 1.17→42.68 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 10.2 / 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: 1.17→42.68 Å
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Refine LS restraints |
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LS refinement shell |
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