[English] 日本語
![](img/lk-miru.gif)
- PDB-1p2j: Structural consequences of accommodation of four non-cognate amin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1p2j | ||||||
---|---|---|---|---|---|---|---|
Title | Structural consequences of accommodation of four non-cognate amino-acid residues in the S1 pocket of bovine trypsin and chymotrypsin | ||||||
![]() |
| ||||||
![]() | hydrolase/hydrolase inhibitor / trypsin / chymotrypsin / serine proteinase / bovine pancreatic trypsin inhibitor / protein-protein interaction / non-cognate binding / S1 pocket / primary specificity / crystal structure / hydrolase-hydrolase inhibitor COMPLEX | ||||||
Function / homology | ![]() trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Helland, R. / Czapinska, H. / Leiros, I. / Olufsen, M. / Otlewski, J. / Smalaas, A.O. | ||||||
![]() | ![]() Title: Structural consequences of accommodation of four non-cognate amino acid residues in the S1 pocket of bovine trypsin and chymotrypsin. Authors: Helland, R. / Czapinska, H. / Leiros, I. / Olufsen, M. / Otlewski, J. / Smalaas, A.O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p2iC ![]() 1p2kC ![]() 1p2mC ![]() 1p2nC ![]() 1p2oC ![]() 1p2qC ![]() 3btgS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
---|---|---|---|
#2: Protein | Mass: 6493.508 Da / Num. of mol.: 1 / Mutation: K15L, M52L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 56.97 % |
---|---|
Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50% ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9312 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→14.98 Å / Num. all: 77696 / Num. obs: 77696 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.81 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 2.4 / Num. unique all: 77728 / Rsym value: 0.209 / % possible all: 64.4 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 3btg Resolution: 1.35→8 Å / Isotropic thermal model: Anisotropical / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Refinement was done using both CNS and SHELX
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.01 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati sigma a obs: 0.16 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→8 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|