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Open data
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Basic information
Entry | Database: PDB / ID: 2ocv | |||||||||
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Title | Structural basis of Na+ activation mimicry in murine thrombin | |||||||||
![]() | (Thrombin) x 2 | |||||||||
![]() | HYDROLASE / SERINE PROTEASE | |||||||||
Function / homology | ![]() Common Pathway of Fibrin Clot Formation / Platelet Aggregation (Plug Formation) / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Intrinsic Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / thrombin-activated receptor signaling pathway / Peptide ligand-binding receptors / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade ...Common Pathway of Fibrin Clot Formation / Platelet Aggregation (Plug Formation) / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Intrinsic Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / thrombin-activated receptor signaling pathway / Peptide ligand-binding receptors / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade / G alpha (q) signalling events / Cell surface interactions at the vascular wall / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / thrombin / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / negative regulation of proteolysis / lipopolysaccharide binding / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of reactive oxygen species metabolic process / peptidase activity / heparin binding / regulation of cell shape / positive regulation of cell growth / regulation of gene expression / collagen-containing extracellular matrix / endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Marino, F. / Chen, Z. / Ergenekan, C.E. / Bush, L.A. / Mathews, F.S. / Di Cera, E. | |||||||||
![]() | ![]() Title: Structural basis of na+ activation mimicry in murine thrombin. Authors: Marino, F. / Chen, Z.W. / Ergenekan, C.E. / Bush-Pelc, L.A. / Mathews, F.S. / Di Cera, E. #1: ![]() Title: Molecular dissection of NA+ binding to thrombin Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / Mathews, F.S. / 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 | ![]() | 78.9 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.4 KB | Display | ![]() |
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Full document | ![]() | 787.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2od3C ![]() 1shhS 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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1 |
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a monomer. |
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Components
#1: Protein/peptide | Mass: 4820.411 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Protein | Mass: 30011.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 295 K / pH: 6.5 Details: 25% PEG 2000 MME, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2006 |
Radiation | Monochromator: APS 14-BM-C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28 Å / Num. obs: 13687 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.2 / % possible all: 80.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB CODE 1SHH Resolution: 2.2→28.03 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 243124.1 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.4 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Total num. of bins used: 6
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