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Yorodumi- PDB-3eq8: Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eq8 | ||||||
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Title | Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type inhibitors | ||||||
Components | Prolyl endopeptidase | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / Hydrolase / Protease / Serine protease / Hydrolase-Hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.73 Å | ||||||
Authors | Kanai, K. / Aranyi, P. / Bocskei, Z. / Ferenczy, G. / Harmat, V. / Simon, K. / Naray-Szabo, G. / Hermecz, I. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Prolyl oligopeptidase inhibition by N-acyl-pro-pyrrolidine-type molecules Authors: Kanai, K. / Aranyi, P. / Bocskei, Z. / Ferenczy, G. / Harmat, V. / Simon, K. / Batori, S. / Naray-Szabo, G. / Hermecz, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eq8.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eq8.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 3eq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eq8 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eq8 | HTTPS FTP |
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-Related structure data
Related structure data | 3eq7C 3eq9C 1qfsS 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: 80864.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: muscle / References: UniProt: P23687, prolyl oligopeptidase |
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#2: Chemical | ChemComp-X98 / |
#3: 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: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17% MPEG 5000, 15% glycerol, 20mM calcium acetate, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 28, 1998 / Details: capillary collimator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.724→34.378 Å / Num. obs: 21070 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 47.11 Å2 / Rmerge(I) obs: 0.177 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.724→2.88 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.521 / Num. unique all: 3047 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1QFS Resolution: 2.73→34.03 Å Isotropic thermal model: Grouped isotropic B-factors, 2 B-values/residue Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37.2 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2729 Å / Luzzati sigma a obs: 0.3156 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→34.03 Å
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Refine LS restraints |
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