[English] 日本語
![](img/lk-miru.gif)
- PDB-3gis: Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gis | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin | ||||||
![]() |
| ||||||
![]() | BLOOD CLOTTING / protein-protein complex / coagulation / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Hydrolase / Kringle / Protease / Secreted / Serine protease / Zymogen / EGF-like domain / Hydroxylation / Membrane / Receptor / Thrombophilia / Transmembrane | ||||||
Function / homology | ![]() blood coagulation, common pathway / apicolateral plasma membrane / negative regulation of blood coagulation / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity ...blood coagulation, common pathway / apicolateral plasma membrane / negative regulation of blood coagulation / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / response to X-ray / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / response to cAMP / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / female pregnancy / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / transmembrane signaling receptor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor activity / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Adams, T.E. / Huntington, J.A. | ||||||
![]() | ![]() Title: Molecular basis of thrombomodulin activation of slow thrombin Authors: Adams, T.E. / Li, W. / Huntington, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 266.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 211.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 533.8 KB | Display | |
Data in XML | ![]() | 52.4 KB | Display | |
Data in CIF | ![]() | 73.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein/peptide , 1 types, 3 molecules ACE
#1: Protein/peptide | Mass: 5641.175 Da / Num. of mol.: 3 / Fragment: Thrombin light-chain, UNP residues 315-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Protein , 2 types, 6 molecules BDFXYZ
#2: Protein | Mass: 29764.219 Da / Num. of mol.: 3 / Fragment: Thrombin heavy-chain, UNP residues 364-622 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 12931.283 Da / Num. of mol.: 3 Fragment: Thrombomodulin EGF domains 4-5-6, UNP residues 363-483 Mutation: M388L,R456G,H457Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 3 types, 593 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.19 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→91.9 Å / Num. all: 60765 / Num. obs: 58334 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 95 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JOU, 1DX5 Resolution: 2.4→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 21.479 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.81 Å2 / Biso mean: 28.213 Å2 / Biso min: 2.83 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|