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Yorodumi- PDB-4bcb: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bcb | ||||||
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Title | PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2- substituted N-acyl-prolylpyrrolidine inhibitor | ||||||
Components | PROLYL ENDOPEPTIDASE | ||||||
Keywords | HYDROLASE / ALPHA-BETA-HYDROLASE / AMNESIA / BETA-PROPELLER / PARKINSONS DISEASE / ALZHEIMERS DISEASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | VanDerVeken, P. / Fulop, V. / Rea, D. / Gerard, M. / VanElzen, R. / Joossens, J. / Cheng, J.D. / Baekelandt, V. / DeMeester, I. / Lambeir, A.M. / Augustyns, K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bcb.cif.gz | 302.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bcb.ent.gz | 245.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bcb_validation.pdf.gz | 778 KB | Display | wwPDB validaton report |
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Full document | 4bcb_full_validation.pdf.gz | 781.5 KB | Display | |
Data in XML | 4bcb_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 4bcb_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/4bcb ftp://data.pdbj.org/pub/pdb/validation_reports/bc/4bcb | HTTPS FTP |
-Related structure data
Related structure data | 4bccC 4bcdC 1qfsS 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: 80864.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: P23687, prolyl oligopeptidase | ||
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#2: Chemical | ChemComp-4I4 / ( Type: Peptide-like / Class: Enzyme inhibitor / Mass: 399.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N6O3 / Details: P2- substituted N-acyl-prolylpyrrolidine inhibitor References: (5R,6R,8S)-8-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-5-CYCLOHEXYL-6-HYDROXY-3-OXO-1-PHENYL-2,7-DIOXA-4-AZA-6-PHOSPHANONAN-9-OIC ACID | ||
#3: Chemical | ChemComp-TAM / | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.5 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 |
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: 1.7→52 Å / Num. obs: 83611 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.7→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFS Resolution: 1.7→51.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.806 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / 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: 22.798 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→51.31 Å
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Refine LS restraints |
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