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- PDB-1e0f: Crystal structure of the human alpha-thrombin-haemadin complex: a... -
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Basic information
Entry | Database: PDB / ID: 1e0f | ||||||
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Title | Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor | ||||||
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![]() | HYDROLASE / COAGULATION/CRYSTAL STRUCTURE/HEPARIN-B / COAGULATION/CRYSTAL STRUCTURE/HEPARIN-BINDING SITE/ HIRUDIN/THROMBIN INHIBITOR | ||||||
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 / 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 / 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 | ![]() ![]() | ||||||
![]() | Richardson, J.L. / Kroeger, B. / Hoefken, W. / Pereira, P. / Huber, R. / Bode, W. / Fuentes-Prior, P. | ||||||
![]() | ![]() Title: Crystal Structure of the Human Alpha-Thrombin-Haemadin Complex: An Exosite II-Binding Inhibitor Authors: Richardson, J.L. / Kroeger, B. / Hoeffken, W. / Sadler, J.E. / Pereira, P. / Huber, R. / Bode, W. / Fuentes-Prior, P. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Isolation, Sequence Analysis, and Cloning of Haemadin an Anticoagulant Peptide from the Indian Leech Authors: Strube, K.-H. / Kroeger, B. / Bialojan, S. / Otte, M. / Dodt, J. #2: ![]() Title: The Refined 1.9 Angstrom X-Ray Crystal Structure of D-Phe-Pro-Arg-Chloromethylketone Inhibited Human Alpha Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed ...Title: The Refined 1.9 Angstrom X-Ray Crystal Structure of D-Phe-Pro-Arg-Chloromethylketone Inhibited Human Alpha Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active Site Geometry and Structure Function Relatioships Authors: Bode, W. / Turk, D. / Karshikov, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.2 KB | Display | ![]() |
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PDB format | ![]() | 174.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420 KB | Display | ![]() |
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Full document | ![]() | 442.6 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4htcS 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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Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: HUMAN THROMBIN WAS PURIFIED FROM HUMAN SERUM ACCORDING TO REPORTED PROTOCOLS Source: (natural) ![]() #2: Protein | Mass: 29792.273 Da / Num. of mol.: 3 / Fragment: NO / Source method: isolated from a natural source Details: HUMAN THROMBIN WAS PURIFIED FROM HUMAN SERUM ACCORDING TO REPORTED PROTOCOLS Source: (natural) ![]() #3: Protein | Mass: 6262.853 Da / Num. of mol.: 3 / Fragment: NO Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: RECOMBINANTLY EXPRESSED IN E. COLI AS A MALTOSE BINDING PROTEIN CONJUGATE Plasmid: PMAL-P2 / Production host: ![]() ![]() #4: Water | ChemComp-HOH / | Sequence details | CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.56 Details: VAPOUR-DIFFUSION SITTING DROP,0.1 M NA CITRATE PH 5.56 14% (W/V) PEG4000, 12.5% (V/V) ISOPROPANOL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusionDetails: drop consists of equal amounts of protein and precipitant solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→32.791 Å / Num. obs: 23938 / Rmerge(I) obs: 0.109 |
Reflection | *PLUS % possible obs: 81.2 % / Num. measured all: 126754 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HTC Resolution: 3.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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