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- PDB-1jmo: Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jmo | |||||||||
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Title | Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex | |||||||||
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![]() | BLOOD CLOTTING / serpin / thrombin / protease / inhibition / inhibitor | |||||||||
Function / homology | ![]() endopeptidase inhibitor activity / 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 ...endopeptidase inhibitor activity / 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 / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor 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) / chemotaxis / 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 | ![]() ![]() ![]() | |||||||||
![]() | Baglin, T.P. / Carrell, R.W. / Esmon, C.T. / Huntington, J.A. | |||||||||
![]() | ![]() Title: Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism. Authors: Baglin, T.P. / Carrell, R.W. / Church, F.C. / Esmon, C.T. / Huntington, J.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.2 KB | Display | ![]() |
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PDB format | ![]() | 132.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 879.7 KB | Display | ![]() |
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Full document | ![]() | 902.5 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 45.3 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/peptide , 1 types, 1 molecules L
#1: Protein/peptide | Mass: 5483.981 Da / Num. of mol.: 1 / Fragment: light chain Source method: isolated from a genetically manipulated source Details: contains extra 13 amino acids at the N-terminus / Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 2 types, 2 molecules HA
#2: Protein | Mass: 29921.414 Da / Num. of mol.: 1 / Fragment: heavy chain / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 55186.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Plasma purified Human Heparin Cofactor II / Source: (natural) ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#4: 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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#7: Sugar |
-Non-polymers , 3 types, 214 molecules ![](data/chem/img/NA.gif)
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#5: Chemical | ChemComp-NA / | ||
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#6: Chemical | ChemComp-MPD / ( #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.68 Å3/Da / Density % sol: 73.75 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: NH4Cl, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2001 / Details: mirrors |
Radiation | Monochromator: liquid gallium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 84555 / Num. obs: 77077 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.081 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.21→2.35 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.5 / Num. unique all: 16159 / Rsym value: 0.434 / % possible all: 62.5 |
Reflection | *PLUS Lowest resolution: 29.4 Å / Num. obs: 77117 / % possible obs: 91.1 % / Num. measured all: 475985 / Rmerge(I) obs: 0.08 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: N-terminal half of native heparin cofactor II and native S195A thrombin Resolution: 2.2→29.44 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target of CNS
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Displacement parameters | Biso mean: 55 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.34 |