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Yorodumi- PDB-5lwt: Endothiapepsin in complex with a methoxylated derivative of fragm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lwt | ||||||
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Title | Endothiapepsin in complex with a methoxylated derivative of fragment 177 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / fragment screening / aspartic protease / inhibition / reactivity | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.069 Å | ||||||
Authors | Schiebel, J. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lwt.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lwt.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lwt_validation.pdf.gz | 474.3 KB | Display | wwPDB validaton report |
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Full document | 5lwt_full_validation.pdf.gz | 474.2 KB | Display | |
Data in XML | 5lwt_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5lwt_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lwt ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lwt | HTTPS FTP |
-Related structure data
Related structure data | 5lwrC 5lwsC 5lwuC 4y5lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 6 types, 322 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DMS / #5: Chemical | #6: Chemical | ChemComp-TFA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.5 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
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: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.069→42.745 Å / Num. obs: 142071 / % possible obs: 99.5 % / Redundancy: 3.695 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.14 |
Reflection shell | Resolution: 1.069→1.13 Å / Redundancy: 3.566 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.29 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y5L Resolution: 1.069→29.437 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.99 / 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: 1.069→29.437 Å
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Refine LS restraints |
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LS refinement shell |
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