+Open data
-Basic information
Entry | Database: PDB / ID: 5dq5 | ||||||
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Title | Endothiapepsin in complex with fragment 209 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / fragment screening / 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 | Radeva, N. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: to be published Title: Crystallographic Fragment Screening of an Entire Library Authors: Radeva, N. / 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 | 5dq5.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dq5.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dq5_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 5dq5_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5dq5_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5dq5_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dq5 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dq5 | HTTPS FTP |
-Related structure data
Related structure data | 3pb5C 3pbdC 3pbzC 3pcwSC 3pgiC 3pi0C 3pldC 3pllC 3pm4C 3pmuC 3pmyC 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
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 / Mutation: 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 | ChemComp-ACT / | ||||
#3: Chemical | #4: Chemical | ChemComp-5HS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
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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: 14.3 / Wavelength: 0.918409 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 24, 2014 |
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→41.018 Å / Num. obs: 54315 / % possible obs: 98.9 % / Redundancy: 3.69 % / Rsym value: 0.06 / Net I/σ(I): 16.42 |
Reflection shell | Resolution: 1.47→1.56 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.55 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PCW Resolution: 1.47→36.493 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.31 / 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→36.493 Å
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Refine LS restraints |
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LS refinement shell |
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