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Open data
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Basic information
Entry | Database: PDB / ID: 3e6p | |||||||||
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Title | Crystal structure of human meizothrombin desF1 | |||||||||
![]() | (Prothrombin) x 2 | |||||||||
![]() | HYDROLASE / Thrombin / meizothrombin / allostery / linkage / Na+ binding / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Secreted / Serine protease / Zymogen | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Papaconstantinou, M.E. / Gandhi, P. / Chen, Z. / Bah, A. / Di Cera, E. | |||||||||
![]() | ![]() Title: Na(+) binding to meizothrombin desF1. Authors: Papaconstantinou, M.E. / Gandhi, P.S. / Chen, Z. / Bah, A. / Di Cera, E. #1: ![]() Title: New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK. Authors: Martin, P.D. / Malkowski, M.G. / Box, J. / Esmon, C.T. / Edwards, B.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.3 KB | Display | ![]() |
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PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules LH
#1: Protein | Mass: 17586.156 Da / Num. of mol.: 1 Fragment: Activation peptide fragment 2 and thrombin light chain: UNP residues 206-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: Thrombin heavy chain: UNP residues 364-622 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 211 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DFK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DFK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / |
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#5: Chemical | ChemComp-DFK / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.2M Na2(SO4), 23% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 43798 / Num. obs: 40469 / % possible obs: 92.4 % / Observed criterion σ(I): -0.5 / Redundancy: 11.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / Num. unique all: 3398 / % possible all: 79 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 1A0H, 1SHH Resolution: 2.1→32.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues L251-L286 were modeled using bovine meizothrombin (PDB ID code 1A0H) and assigned an occupancy of zero due to lack of ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues L251-L286 were modeled using bovine meizothrombin (PDB ID code 1A0H) and assigned an occupancy of zero due to lack of electron density. 3. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and were modeled as alanines.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→32.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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