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Yorodumi- PDB-1h2z: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h2z | ||||||
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Title | PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO | ||||||
Components | PROLYL ENDOPEPTIDASE | ||||||
Keywords | HYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/ BETA-HYDROLASE / BETA-PROPELLER / SERINE PROTEASE | ||||||
Function / homology | Function and homology information prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Rea, D. / Fulop, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Electrostatic Effects and Binding Determinants in the Catalysis of Prolyl Oligopeptidase: Site Specific Mutagenesis at the Oxyanion Binding Site Authors: Szeltner, Z. / Rea, D. / Renner, V. / Fulop, V. / Polgar, L. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Binding for Titration of the Catalytic Histidine Residue Authors: Fulop, V. / Szeltner, Z. / Renner, V. / Polgar, L. #2: Journal: Embo Rep. / Year: 2000 Title: Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism Authors: Fulop, V. / Szeltner, Z. / Polgar, L. #3: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis Authors: Fulop, V. / Bocskei, Z. / Polgar, L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h2z.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h2z.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h2z ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h2z | HTTPS FTP |
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-Related structure data
Related structure data | 1h2wC 1h2xC 1h2yC 1qfmS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 80848.344 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION SER 554 ALA / Source: (gene. exp.) SUS SCROFA (pig) / Tissue: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23687, prolyl oligopeptidase |
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-Non-polymers , 5 types, 1061 molecules
#2: Chemical | ChemComp-GLY / | ||
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#3: Chemical | ChemComp-PRO / | ||
#4: Chemical | ChemComp-SIN / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CLEAVES PEPTIDE BONDS ON THE C-TERMINAL SIDE OF PROLYL RESIDUES WITHIN PEPTIDES OF UP TO ...CLEAVES PEPTIDE BONDS ON THE C-TERMINAL SIDE OF PROLYL RESIDUES WITHIN PEPTIDES OF UP TO APPROXIMAT |
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-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 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: SEE REFERENCE 3, pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Fulop, V., (1998) Cell, 94, 161. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→52 Å / Num. obs: 95461 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.5 / % possible all: 96.9 |
Reflection | *PLUS Lowest resolution: 52 Å / Num. measured all: 472928 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFM Resolution: 1.65→52 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 12.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→52 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 4.1 % / Rfactor all: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |