[English] 日本語
![](img/lk-miru.gif)
- PDB-4jk5: Human urokinase-type Plasminogen Activator (uPA) in complex with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4jk5 | ||||||
---|---|---|---|---|---|---|---|
Title | Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Ser) | ||||||
![]() |
| ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / serine protease / chymotrypsin fold / urokinase-type plasminogen activator / bicyclic peptide inhibitor / D-amino acid / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() Synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Buth, S.A. / Leiman, P.G. / Chen, S. / Heinis, C. | ||||||
![]() | ![]() Title: Improving binding affinity and stability of Peptide ligands by substituting glycines with d-amino acids. Authors: Chen, S. / Gfeller, D. / Buth, S.A. / Michielin, O. / Leiman, P.G. / Heinis, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jk6C ![]() 2nwnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 27586.420 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: C122A, N145Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Protein/peptide | |
-Non-polymers , 5 types, 112 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/ZBR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/ZBR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-P6G / | #6: Chemical | ChemComp-ZBR / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.01 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 50mM Na3(cit) pH 4.9, 5% v/v PEG400, 1.8M (NH4)2SO4, 0.05% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2012 / Details: mirrors |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry and a toroidal mirror (M2) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→33.09 Å / Num. all: 33910 / Num. obs: 33907 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 18.94 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.019 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7729 / Rsym value: 0.217 / % possible all: 99.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NWN Resolution: 1.55→33.09 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.008 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.459 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→33.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
|