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- PDB-5lwu: Structure resulting from an endothiapepsin crystal soaked with a ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lwu | ||||||
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Title | Structure resulting from an endothiapepsin crystal soaked with a dimeric derivative of fragment 177 | ||||||
![]() | Endothiapepsin![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schiebel, J. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring. Authors: Cramer, J. / Schiebel, J. / Wulsdorf, T. / Grohe, K. / Najbauer, E.E. / Ehrmann, F.R. / Radeva, N. / Zitzer, N. / Linne, U. / Linser, R. / 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 | ![]() | 201.8 KB | Display | ![]() |
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PDB format | ![]() | 163.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lwrC ![]() 5lwsC ![]() 5lwtC ![]() 4y5lS 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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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 , 5 types, 334 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/TFA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TFA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
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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![]() |
Reflection | Resolution: 1.109→42.629 Å / Num. obs: 128260 / % possible obs: 99.6 % / Redundancy: 3.712 % / Biso Wilson estimate: 10.296 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.46 |
Reflection shell | Resolution: 1.11→1.18 Å / Redundancy: 3.619 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.34 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4Y5L Resolution: 1.109→39.766 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12.21 / 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: 1.109→39.766 Å
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Refine LS restraints |
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LS refinement shell |
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