[English] 日本語
![](img/lk-miru.gif)
- PDB-1lmw: LMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethy... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1lmw | ||||||
---|---|---|---|---|---|---|---|
Title | LMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethyl Ketone) | ||||||
![]() | (UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2 | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / FIBRINOLYSIS / TRYPSIN-LIKE SERINE PROTEASE / SERINE PROTEASE / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Spraggon, G.S. / Phillips, C. / Nowak, U.K. / Ponting, C.P. / Saunders, D. / Dobson, C.M. / Stuart, D.I. / Jones, E.Y. | ||||||
![]() | ![]() Title: The crystal structure of the catalytic domain of human urokinase-type plasminogen activator. Authors: Spraggon, G. / Phillips, C. / Nowak, U.K. / Ponting, C.P. / Saunders, D. / Dobson, C.M. / Stuart, D.I. / Jones, E.Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 111.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 523.7 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 2708.183 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 28478.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | Compound details | THE STRUCTURE IS THAT OF THE ACTIVE, TWO CHAIN FORM OF THE ENZYME. | Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETH | Sequence details | THE RESIDUES IN THE STRUCTURE ARE NUMBERED, AS IS CONVENTIONAL WITH SERINE PROTEASES, AS ...THE RESIDUES IN THE STRUCTURE ARE NUMBERED, AS IS CONVENTION | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 15684 / % possible obs: 70 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.111 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 54540 / Rmerge(I) obs: 0.111 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→30 Å Details: THE 23 RESIDUES OF THE SHORT A CHAIN IN EACH SUBUNIT ARE HIGHLY MOBILE. RESIDUES 147 - 152 (1 - 6 AS CHYMOTRYPSIN EQUIVALENTS) ARE MODELED IN DENSITY, 153 AND 154 FITTED TENTATIVELY IN WEAK ...Details: THE 23 RESIDUES OF THE SHORT A CHAIN IN EACH SUBUNIT ARE HIGHLY MOBILE. RESIDUES 147 - 152 (1 - 6 AS CHYMOTRYPSIN EQUIVALENTS) ARE MODELED IN DENSITY, 153 AND 154 FITTED TENTATIVELY IN WEAK DENSITY WHILE THE REMAINDER ARE ABSENT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2 |