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- PDB-4amz: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4amz | ||||||
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Title | PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-2 | ||||||
![]() | PROLYL ENDOPEPTIDASE | ||||||
![]() | HYDROLASE / ALPHA/BETA-HYDROLASE / AMNESIA / BETA-PROPELLER | ||||||
Function / homology | ![]() prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kaszuba, K. / Rog, T. / Danne, R. / Canning, P. / Fulop, V. / Juhasz, T. / Szeltner, Z. / St-Pierre, J.F. / Garcia-Horsman, A. / Mannisto, P.T. ...Kaszuba, K. / Rog, T. / Danne, R. / Canning, P. / Fulop, V. / Juhasz, T. / Szeltner, Z. / St-Pierre, J.F. / Garcia-Horsman, A. / Mannisto, P.T. / Karttunen, M. / Hokkanen, J. / Bunker, A. | ||||||
![]() | ![]() Title: Molecular Dynamics, Crystallography and Mutagenesis Studies on the Substrate Gating Mechanism of Prolyl Oligopeptidase. Authors: Kaszuba, K. / Rog, T. / Danne, R. / Canning, P. / Fulop, V. / Juhasz, T. / Szeltner, Z. / St-Pierre, J.F. / Garcia-Horsman, A. / Mannisto, P.T. / Karttunen, M. / Hokkanen, J. / Bunker, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.5 KB | Display | ![]() |
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PDB format | ![]() | 244.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.9 KB | Display | ![]() |
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Full document | ![]() | 755.4 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4amyC ![]() 4an0C ![]() 4an1C ![]() 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-2P4 / ( | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Nonpolymer details | LIGAND 2P4 COVALENTLY | |
-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: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 53794 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QFS Resolution: 2→29.92 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.414 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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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: 17.511 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.92 Å
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Refine LS restraints |
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