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Open data
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Basic information
Entry | Database: PDB / ID: 6bjr | ||||||||||||
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Title | Crystal structure of prothrombin mutant S101C/A470C | ||||||||||||
![]() | Prothrombin | ||||||||||||
![]() | HYDROLASE / Full-length prothrombin / Kringle / closed conformation | ||||||||||||
Function / homology | ![]() 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 ...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 / 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 / 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 / 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 / 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) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / 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 / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Chinnaraj, M. / Chen, Z. / Pelc, L. / Grese, Z. / Bystranowska, D. / Di Cera, E. / Pozzi, N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of prothrombin in the closed form reveals new details on the mechanism of activation. Authors: Chinnaraj, M. / Chen, Z. / Pelc, L.A. / Grese, Z. / Bystranowska, D. / Di Cera, E. / Pozzi, N. #1: ![]() Title: How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. Authors: Pozzi, N. / Chen, Z. / Di Cera, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.1 KB | Display | ![]() |
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PDB format | ![]() | 92.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.6 KB | Display | ![]() |
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Full document | ![]() | 732.1 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c2wC ![]() 5edmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 66309.875 Da / Num. of mol.: 1 / Mutation: S101C, A470C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-MG / #4: Sugar | ChemComp-NAG / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 100 mM Bicine, pH 8.5 and 16% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2017 |
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: 6→40 Å / Num. obs: 2633 / % possible obs: 87.6 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -1.5 / Redundancy: 9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 6→6.2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 167 / % possible all: 59.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EDM Resolution: 6→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / σ(F): -1.5 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 6→40 Å
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Refine LS restraints |
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