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Yorodumi- PDB-4rn6: Structure of prethrombin-2 mutant s195a bound to the active site ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rn6 | |||||||||
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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 / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
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. | |||||||||
Citation | 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. #1: Journal: Biochemistry / Year: 2011 Title: Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation. Authors: Pozzi, N. / Chen, Z. / Zapata, F. / Pelc, L.A. / Barranco-Medina, S. / Di Cera, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rn6.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rn6.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 4rn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/4rn6 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/4rn6 | HTTPS FTP |
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-Related structure data
Related structure data | 4h6sC 4h6tC 4hfpC 3sqhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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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
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Displacement parameters | Biso mean: 30.03 Å2
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Refinement step | Cycle: LAST / Resolution: 3→32.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Total num. of bins used: 20
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