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- PDB-4dih: X-ray structure of the complex between human alpha thrombin and t... -
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Basic information
Entry | Database: PDB / ID: 4dih | ||||||
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Title | X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR/DNA / protein-DNA complex / serine protease / blood coagulation / aptamer / hydrolase-hydrolase inhibitor-DNA complex / serine protease fold / DNA aptamer / blood / G-quadruplex | ||||||
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 DNA (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Russo Krauss, I. / Merlino, A. / Mazzarella, L. / Sica, F. | ||||||
![]() | ![]() Title: High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. Authors: Russo Krauss, I. / Merlino, A. / Randazzo, A. / Novellino, E. / Mazzarella, L. / Sica, F. #1: ![]() Title: Thrombin-aptamer recognition: a revealed ambiguity. Authors: Russo Krauss, I. / Merlino, A. / Giancola, C. / Randazzo, A. / Mazzarella, L. / Sica, F. #2: ![]() Title: The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. Authors: Padmanabhan, K. / Padmanabhan, K.P. / Ferrara, J.D. / Sadler, J.E. / Tulinsky, A. #3: ![]() Title: An ambiguous structure of a DNA 15-mer thrombin complex. Authors: Padmanabhan, K. / Tulinsky, 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 | ![]() | 90.4 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 812.7 KB | Display | ![]() |
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Full document | ![]() | 821.4 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4diiC ![]() 1haoS ![]() 3qlpS C: citing same article ( S: Starting model for refinement |
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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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Details | 1:1 protein-DNA aptamer complex |
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Components
-Protein/peptide / Protein / DNA chain / Sugars , 4 types, 4 molecules LHD![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: Light chain fragment (UNP Residues 328-363) / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: Heavy chain fragment (UNP Residues 364-622) / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: DNA chain | Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others) |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 225 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/0G6.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0G6.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-0G6 / | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER ...THE INHIBITOR IS COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 10-15% w/v polyethylene glycol 8000, 0.05 M zinc acetate, 0.1 M sodium cacodylate , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 11, 2010 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 28160 / Num. obs: 28160 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 75.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QLP AND 1HAO Resolution: 1.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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