|Entry||Database: PDB / ID: 4rn6|
|Title||Structure of prethrombin-2 mutant s195a bound to the active site inhibitor argatroban|
|Components||Thrombin heavy chain|
|Keywords||HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / PRETHROMBIN-2 / AUTOACTIVATION / HYDROLASE-HYDROLASE INHIBITOR complex|
|Function / homology|
Function and homology information
positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / cytolysis by host of symbiont cells / thrombin / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / cytolysis by host of symbiont cells / thrombin / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of fibrinolysis / negative regulation of cytokine production involved in inflammatory response / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / positive regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Peptide ligand-binding receptors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of release of sequestered calcium ion into cytosol / Intrinsic Pathway of Fibrin Clot Formation / fibrinolysis / Thrombin signalling through proteinase activated receptors (PARs) / lipopolysaccharide binding / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / negative regulation of proteolysis / growth factor activity / response to wounding / positive regulation of protein localization to nucleus / platelet activation / G alpha (q) signalling events / Golgi lumen / multicellular organism development / positive regulation of reactive oxygen species metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / positive regulation of cell growth / collagen-containing extracellular matrix / regulation of cell shape / blood microparticle / cell surface receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of protein phosphorylation / proteolysis / signaling receptor binding / serine-type endopeptidase activity / endoplasmic reticulum lumen / calcium ion binding / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin light chain domain superfamily / Thrombin light chain / Prothrombin/thrombin / Thrombin light chain / Kringle domain / Kringle domain profile. / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle ...Thrombin light chain domain superfamily / Thrombin light chain / Prothrombin/thrombin / Thrombin light chain / Kringle domain / Kringle domain profile. / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Domain containing Gla (gamma-carboxyglutamate) residues. / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Gla domain profile. / Vitamin K-dependent carboxylation domain. / Gamma-carboxyglutamic acid-rich (GLA) domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
S-argatroban / Chem-15U / Prothrombin
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å|
|Authors||Pozzi, N. / Chen, Z. / Zapata, F. / Niu, W. / Barranco-Medina, S. / Pelc, L.A. / Di Cera, E.|
Journal: J.Biol.Chem. / Year: 2013
Title: Autoactivation of thrombin precursors.
Authors: Pozzi, N. / Chen, Z. / Zapata, F. / Niu, W. / Barranco-Medina, S. / Pelc, L.A. / Di Cera, E.
|Structure viewer||Molecule: |
Downloads & links
A: Thrombin heavy chain
B: Thrombin heavy chain
A: Thrombin heavy chain
B: Thrombin heavy chain
Mass: 33393.270 Da / Num. of mol.: 2 / Fragment: UNP residues 333-622 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 %|
|Crystal grow||Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 |
Details: 100 mM TRIS PH 8.5, 200 mM LI2SO4 AND 30% PEG 3000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å|
|Detector||Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2012|
|Radiation||Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||Resolution: 3→32.13 Å / Num. all: 11154 / Num. obs: 10552 / % possible obs: 94.6 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 5.9|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 3SQH
Resolution: 3→32.13 Å / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
|Displacement parameters||Biso mean: 30.03 Å2|
|Refinement step||Cycle: LAST / Resolution: 3→32.13 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 3→3.08 Å / Total num. of bins used: 20 |
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