+Open data
-Basic information
Entry | Database: PDB / ID: 4y5g | ||||||
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Title | Endothiapepsin in complex with fragment 272 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / fragment screening / aspartic protease / inhibition | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Wang, X. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: to be published Title: Crystallographic Fragment Sreening of an Entire Library Authors: Wang, X. / Heine, A. / Klebe, G. #1: Journal: J. Med. Chem. / Year: 2011 Title: A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes. Authors: Koester, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / 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 | 4y5g.cif.gz | 194 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y5g.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 4y5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/4y5g ftp://data.pdbj.org/pub/pdb/validation_reports/y5/4y5g | HTTPS FTP |
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-Related structure data
Related structure data | 4y3aC 4y3hC 4y3lC 4y3tC 4y58C 4y5aC 4y5bC 4y5cC 4y5eC 4y5kC 3pcwS C: citing same article (ref.) S: Starting model for refinement |
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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 , 5 types, 286 molecules
#2: Chemical | ChemComp-47U / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.61 % |
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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: Jul 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→42.759 Å / Num. obs: 51878 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rsym value: 0.049 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.47→1.56 Å / Redundancy: 2.31 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.5 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PCW Resolution: 1.47→42.759 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.84 / 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: 1.47→42.759 Å
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Refine LS restraints |
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LS refinement shell |
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