+Open data
-Basic information
Entry | Database: PDB / ID: 4l6b | ||||||
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Title | Endothiapepsin in complex with thiophen-based inhibitor SAP128 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ASPARTATE PROTEASE / Inhibitor Complex / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Park, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Endothiapepsin in Complex with Thiophen based Inhibitors Authors: Kuhnert, M. / Park, A. / Heine, A. / 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 | 4l6b.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l6b.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 4l6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/4l6b ftp://data.pdbj.org/pub/pdb/validation_reports/l6/4l6b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 / Fragment: UNP residues 90-419 / 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: Chemical | ChemComp-1VS / | #4: Chemical | ChemComp-GOL / | #5: 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: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M NH4AC, 0.1M ACETATE-BUFFER, 26% PEG4000, , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Monochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→30 Å / Num. all: 68886 / Num. obs: 68886 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.092 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3442 / Rsym value: 0.486 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→30 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.97 / Stereochemistry target values: Engh & Huber
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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: 1.37→30 Å
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Refine LS restraints |
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LS refinement shell |
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