[English] 日本語
![](img/lk-miru.gif)
- PDB-1gj7: ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER19... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1gj7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS | |||||||||
![]() | (UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2 | |||||||||
![]() | BLOOD CLOTTING / hydrolase / selectivity at S1 / H2O displacement / uPA / tPA / Ser190/Ala190 protease / structure-based drug design | |||||||||
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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L. | |||||||||
![]() | ![]() Title: Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets. Authors: Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Elrod, K. / Kirtley, M. / Janc, J. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 727.4 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gj4C ![]() 1gj5C ![]() 1gj6C ![]() 1gj8C ![]() 1gj9C ![]() 1gjaC ![]() 1gjbC ![]() 1gjcC ![]() 1gjdC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein/peptide | Mass: 2708.183 Da / Num. of mol.: 1 / Fragment: SHORT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 28435.428 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: N145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-132 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.16 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 2-propanol PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Katz, B.A., (2000) Chem.Biol., 7, 299. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→38.31 Å / Num. all: 57517 / Num. obs: 31833 / % possible obs: 55.3 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.41→1.53 Å / Rmerge(I) obs: 0.318 / Num. unique all: 3274 / % possible all: 31.8 |
Reflection | *PLUS Num. obs: 27459 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues ...Details: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues simultaneously refined in two or more conformations are: Lys_A10, Ile_B16, Glu_B25, Met_B47, Glu_B84, Glu_B86, Thr_B139, Gln_B192, Leu_B209, Pro_B225, Leu_B235 Disordered waters are: HOH119 which is close to a symmetry-related equivalent of itself; HOH373 which is close to HOH374; HOH584 which is close to a symmetry-related equivalent of itself; HOH806 which is close to HOH807; No energy terms between citrate 1 and 2 are included because they are hydrogen-bonded to one another via an unusually short hydrogen bond between carboxylate / hydroxyl groups.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→7 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / % reflection Rfree: 10 % / Rfactor all: 0.203 / Rfactor obs: 0.165 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.165 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rwork: 0.203 / Rfactor obs: 0.203 |