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- PDB-4bcd: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bcd | ||||||
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Title | PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BOUND P2-substituted N-acyl-prolylpyrrolidine inhibitor | ||||||
![]() | PROLYL ENDOPEPTIDASE | ||||||
![]() | HYDROLASE / ALPHA-BETA-HYDROLASE / AMNESIA / PARKINSONS DISEASE / ALZHEIMERS DISEASE / INHIBITOR | ||||||
Function / homology | ![]() prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | VanDerVeken, P. / Fulop, V. / Rea, D. / Gerard, M. / VanElzen, R. / Joossens, J. / Cheng, J.D. / Baekelandt, V. / DeMeester, I. / Lambeir, A.M. / Augustyns, K. | ||||||
![]() | ![]() Title: P2-Substituted N-Acylprolylpyrrolidine Inhibitors of Prolyl Oligopeptidase: Biochemical Evaluation, Binding Mode Determination, and Assessment in a Cellular Model of Synucleinopathy. Authors: Van Der Veken, P. / Fulop, V. / Rea, D. / Gerard, M. / Van Elzen, R. / Joossens, J. / Cheng, J.D. / Baekelandt, V. / De Meester, I. / Lambeir, A.M. / Augustyns, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.5 KB | Display | ![]() |
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PDB format | ![]() | 247.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 746.3 KB | Display | ![]() |
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Full document | ![]() | 750.2 KB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 57.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bcbC ![]() 4bccC ![]() 1qfsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-TDV / ![]() References: 1-[(2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-pyrrolidin-1-ylcarbonyl-pyrrolidin-1-yl]-4-phenyl-butan-1-one | ||
#3: Chemical | ChemComp-TAM / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 18-20% METHOXY-POLYETHYLENE GLYCOL (MPEG) 5K, 20 MM CA(OAC)2, 0.1 M TRIS PH 8.5, 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9702 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→56 Å / Num. obs: 120401 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QFS Resolution: 1.5→55.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.277 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.925 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→55.47 Å
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Refine LS restraints |
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