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- PDB-7zko: X-ray structure of the complex between human alpha thrombin and a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zko | ||||||
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Title | X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form delta | ||||||
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![]() | HYDROLASE / Thrombin / Aptamer / Complex / Inhibitor / Coagulation | ||||||
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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Troisi, R. / Sica, F. | ||||||
Funding support | 1items
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![]() | ![]() Title: A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Authors: Troisi, R. / Riccardi, C. / Perez de Carvasal, K. / Smietana, M. / Morvan, F. / Del Vecchio, P. / Montesarchio, D. / Sica, 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 | ![]() | 92.1 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zklC ![]() 7zkmC ![]() 7zknC ![]() 1ppbS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 / Protein / DNA chain , 3 types, 4 molecules LHAB
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: DNA chain | Mass: 4743.051 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The correct sequence alignment for chain A is: --------10----- GGTTGGTGTGGTTGG ||||||--||||||| GGTTGG..TGGTTGG The correct sequence alignment for chain B is: --------10----- GGTTGGTGTGGTTGG - ...Details: The correct sequence alignment for chain A is: --------10----- GGTTGGTGTGGTTGG ||||||--||||||| GGTTGG..TGGTTGG The correct sequence alignment for chain B is: --------10----- GGTTGGTGTGGTTGG -||||-----||||- .GTTG.....GTTG. Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 20 molecules ![](data/chem/img/0G6.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/JL0.gif)
![](data/chem/img/JKR.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/JL0.gif)
![](data/chem/img/JKR.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-0G6 / |
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#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-JL0 / |
#7: Chemical | ChemComp-JKR / |
#8: Chemical | ChemComp-K / |
#9: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350 30% w/v, 0.2 M sodium malonate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.02 Å / Num. obs: 17665 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 1 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 896 / CC1/2: 0.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PPB Resolution: 2.5→49.02 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.872 / SU B: 13.615 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 148.08 Å2 / Biso mean: 77.887 Å2 / Biso min: 42.6 Å2
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Refinement step | Cycle: final / Resolution: 2.5→49.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0
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