[English] 日本語
![](img/lk-miru.gif)
- PDB-1o6g: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641N MUTANT WITH BOUND... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1o6g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641N MUTANT WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO | |||||||||
![]() | Prolyl endopeptidase | |||||||||
![]() | HYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/ BETA-HYDROLASE / BETA-PROPELLER | |||||||||
Function / homology | ![]() prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rea, D. / Fulop, V. | |||||||||
![]() | ![]() Title: Substrate-dependent competency of the catalytic triad of prolyl oligopeptidase. Authors: Szeltner, Z. / Rea, D. / Juhasz, T. / Renner, V. / Mucsi, Z. / Orosz, G. / Fulop, V. / Polgar, L. #1: ![]() Title: Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Bindtitration of the Catalytic Histidine Residueing for Authors: Fulop, V. / Szeltner, Z. / Renner, V. / Polgar, L. #2: ![]() Title: Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism Authors: Fulop, V. / Szeltner, Z. / Polgar, L. #3: ![]() Title: Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis Authors: Fulop, V. / Bocskei, Z. / Polgar, L. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 179.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1o6fC ![]() 1qfmS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 80891.414 Da / Num. of mol.: 1 / Mutation: D641N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-SIN / |
#3: Chemical | ChemComp-GLY / |
#4: Chemical | ChemComp-PRO / |
#5: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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(Cambridge,Mass.), 94, 161. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2001 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 156733 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 4.7 / % possible all: 97.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 686744 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QFM Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 4 % / Rfactor all: 0.203 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |