[English] 日本語
![](img/lk-miru.gif)
- PDB-6o1s: Structure of human plasma kallikrein protease domain with inhibitor -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6o1s | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human plasma kallikrein protease domain with inhibitor | |||||||||
![]() | Plasma kallikrein | |||||||||
![]() | BLOOD CLOTTING / Protease | |||||||||
Function / homology | ![]() plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Partridge, J.R. / Choy, R.M. | |||||||||
![]() | ![]() Title: Structures of full-length plasma kallikrein bound to highly specific inhibitors describe a new mode of targeted inhibition. Authors: Partridge, J.R. / Choy, R.M. / Silva-Garcia, A. / Yu, C. / Li, Z. / Sham, H. / Metcalf, B. #1: ![]() Title: Structure-Guided Design of Novel, Potent, and Selective Macrocyclic Plasma Kallikrein Inhibitors. Authors: Li, Z. / Partridge, J. / Silva-Garcia, A. / Rademacher, P. / Betz, A. / Xu, Q. / Sham, H. / Hu, Y. / Shan, Y. / Liu, B. / Zhang, Y. / Shi, H. / Xu, Q. / Ma, X. / Zhang, L. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 95.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 724.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 730.3 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bfpC ![]() 6o1gC ![]() 2anwS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29427.314 Da / Num. of mol.: 1 / Mutation: N377E, N434E, N475E, C383E, and C484S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-7SD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.51 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 24% PEG 3350, 0.2M potassium dihydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 31089 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 21.9 Å2 / Rpim(I) all: 0.032 / Rsym value: 0.092 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 4.1 / Rpim(I) all: 0.339 / Rsym value: 0.977 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ANW Resolution: 1.7→27.842 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.64 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→27.842 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -17.9546 Å / Origin y: -9.5999 Å / Origin z: 13.7136 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |