[English] 日本語
![](img/lk-miru.gif)
- PDB-1hut: THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1hut | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER | ||||||
![]() |
| ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR/DNA / THROMBIN / BLOOD CLOTTING / HYDROLASE-HYDROLASE INHIBITOR-DNA COMPLEX | ||||||
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 | ![]() | ||||||
![]() | Padmanabhan, K. / Padmanabhan, K.P. / Ferrara, J.D. / Sadler, J.E. / Tulinsky, A. | ||||||
![]() | ![]() 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 552.4 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 364-622 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Chemical | ChemComp-0G7 / |
#5: Water | ChemComp-HOH / |
Sequence details | CHYMOTRYPSIN NUMBERING SYSTEM IS USED BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7.3 / Method: vapor diffusion, hanging drop / Details: Skrzypczak, J., (1991) J. Mol. Biol., 221, 1379. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ![]() |
---|---|
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.87 Å / Num. obs: 6990 |
Reflection | *PLUS % possible obs: 67 % / Observed criterion σ(F): 1 / Num. measured all: 12408 / Rmerge F obs: 0.116 |
Reflection shell | *PLUS Highest resolution: 2.87 Å / Lowest resolution: 2.9 Å / % possible obs: 32 % |
-
Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Highest resolution: 2.9 Å /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.159 / Rfactor Rwork: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.3 |