+Open data
-Basic information
Entry | Database: PDB / ID: 3pmy | ||||||
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Title | Endothiapepsin in complex with a fragment | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / 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: 1.38 Å | ||||||
Authors | Koester, H. / Heine, A. / Klebe, G. | ||||||
Citation | 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: Koster, 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 | 3pmy.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pmy.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pmy_validation.pdf.gz | 724.9 KB | Display | wwPDB validaton report |
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Full document | 3pmy_full_validation.pdf.gz | 726 KB | Display | |
Data in XML | 3pmy_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3pmy_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/3pmy ftp://data.pdbj.org/pub/pdb/validation_reports/pm/3pmy | HTTPS FTP |
-Related structure data
Related structure data | 3pb5C 3pbdC 3pbzC 3pcwC 3pgiC 3pi0C 3pldC 3pllC 3pm4C 3pmuC 1oewS 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
#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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#2: Chemical | ChemComp-41L / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-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: 49.6 % |
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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 277K, temperature 289K |
-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: RAYONIX MX-225 / Detector: CCD / Date: Oct 21, 2010 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→30 Å / Num. all: 65186 / Num. obs: 65186 / % possible obs: 100 % / Redundancy: 3 % / Rsym value: 0.046 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2882 / Rsym value: 0.219 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1OEW Resolution: 1.38→10 Å / Num. parameters: 24384 / Num. restraintsaints: 30397 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 2240 / Occupancy sum non hydrogen: 2686 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→10 Å
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Refine LS restraints |
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