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Yorodumi- PDB-3psy: Endothiapepsin in complex with an inhibitor based on the Gewald r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3psy | ||||||
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Title | Endothiapepsin in complex with an inhibitor based on the Gewald reaction | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Koester, H. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors. Authors: Kuhnert, M. / Koster, H. / Bartholomaus, R. / Park, A.Y. / Shahim, A. / Heine, A. / Steuber, H. / Klebe, G. / Diederich, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3psy.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3psy.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 3psy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3psy_validation.pdf.gz | 759.1 KB | Display | wwPDB validaton report |
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Full document | 3psy_full_validation.pdf.gz | 760.7 KB | Display | |
Data in XML | 3psy_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3psy_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/3psy ftp://data.pdbj.org/pub/pdb/validation_reports/ps/3psy | HTTPS FTP |
-Related structure data
Related structure data | 3wz6C 3wz7C 3wz8C 1oewS 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, EC: 3.4.23.22 |
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-Non-polymers , 6 types, 240 molecules
#2: Chemical | ChemComp-RB9 / |
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#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-PG4 / |
#6: Chemical | ChemComp-1PE / |
#7: Water | ChemComp-HOH / |
-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: 49.64 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M NH4Ac, 0.1M Acetate-Buffer pH 4.6, 26% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2009 / Details: mirrors |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→40 Å / Num. all: 55570 / Num. obs: 55570 / % possible obs: 100 % / Redundancy: 3.5 % / Rsym value: 0.034 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 2578 / Rsym value: 0.285 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OEW Resolution: 1.43→10 Å / Num. parameters: 24349 / Num. restraintsaints: 30620 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 2239.64 / Occupancy sum non hydrogen: 2676.32 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→10 Å
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Refine LS restraints |
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