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- PDB-1bth: STRUCTURE OF THROMBIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN IN... -
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Basic information
Entry | Database: PDB / ID: 1bth | ||||||
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Title | STRUCTURE OF THROMBIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR | ||||||
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![]() | COMPLEX (SERINE PROTEASE/INHIBITOR) / THROMBIN INHIBITOR / SERINE PROTEINASE KUNITZ-LIKE INHIBITOR / (SERINE PROTEASE/INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) COMPLEX | ||||||
Function / homology | ![]() trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function 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 ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function 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 / negative regulation of thrombin-activated receptor signaling pathway / 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 / serine protease inhibitor complex / 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 / 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) / 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 / protease binding / 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 | ![]() | ||||||
![]() | Van De Locht, A. / Bode, W. / Stubbs, M.T. | ||||||
![]() | ![]() Title: The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin. Authors: van de Locht, A. / Bode, W. / Huber, R. / Le Bonniec, B.F. / Stone, S.R. / Esmon, C.T. / Stubbs, M.T. #1: ![]() Title: The Ornithodorin-Thrombin Crystal Structure, a Key to the Tap Enigma? Authors: Van De Locht, A. / Stubbs, M.T. / Bode, W. / Friedrich, T. / Bollschweiler, C. / Hoffken, W. / Huber, R. #2: ![]() Title: Two Heads are Better Than One: Crystal Structure of the Insect Derived Double Domain Kazal Inhibitor Rhodniin in Complex with Thrombin Authors: Van De Locht, A. / Lamba, D. / Bauer, M. / Huber, R. / Friedrich, T. / Kroger, B. / Hoffken, W. / Bode, W. #3: ![]() Title: The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.7 KB | Display | ![]() |
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PDB format | ![]() | 125.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 401.2 KB | Display | ![]() |
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Full document | ![]() | 416.7 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 2 / Mutation: E192Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 29809.262 Da / Num. of mol.: 2 / Mutation: E192Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 6527.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 52 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 7 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 109248 / % possible obs: 0.983 % / Observed criterion σ(I): 3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. obs: 37833 / % possible obs: 0.994 % / Num. measured all: 98344 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.303 |
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Processing
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Refinement | Resolution: 2.3→6 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |