+Open data
-Basic information
Entry | Database: PDB / ID: 5sar | ||||||
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Title | Endothiapepsin in complex with compound FU290-1 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / Frag4Lead / fragment screening / hydrolase / inhibition / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.98 Å | ||||||
Authors | Wollenhaupt, J. / Metz, A. / Messini, N. / Barthel, T. / Klebe, G. / Weiss, M.S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Authors: Metz, A. / Wollenhaupt, J. / Glockner, S. / Messini, N. / Huber, S. / Barthel, T. / Merabet, A. / Gerber, H.D. / Heine, A. / Klebe, G. / Weiss, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sar.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sar.ent.gz | 167.7 KB | Display | PDB format |
PDBx/mmJSON format | 5sar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5sar_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5sar_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5sar_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5sar_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/5sar ftp://data.pdbj.org/pub/pdb/validation_reports/sa/5sar | HTTPS FTP |
-Group deposition
ID | G_1002201 (10 entries) |
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Title | Endothiapepsin with Frag4Lead follow-up compounds |
Type | undefined |
Description | Complexes of Endothiapepsin and follow-up compounds from Frag4Lead campaign |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43278.664 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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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M NaAc pH 4.6, 0.1 M NH4Ac pH 7.0, 27% (w/v) PEG 4000, 1.5µL protein + 1.5µL reservoir + 0.1µL seeds Seeding: seeds obtained from crystals of same condition using 24-33% PEG 4000, diluted to 1:15 -1:45 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.98→41.13 Å / Num. obs: 175062 / % possible obs: 94.4 % / Redundancy: 3.814 % / Biso Wilson estimate: 12.116 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.135 / Χ2: 1.04 / Net I/σ(I): 5.47 / Num. measured all: 667615 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 0.98→41.13 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.962 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→41.13 Å
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Refine LS restraints |
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LS refinement shell |
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