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Yorodumi- PDB-1g37: CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH BCH-1055... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g37 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH BCH-10556 AND EXOSITE-DIRECTED PEPTIDE | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / protease / thrombin / inhibitor / blood clotting / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Isomorphous with other thrombin complexes / Resolution: 2 Å | ||||||
Authors | Bachand, B. / Tarazi, M. / St-Denis, Y. / Edmunds, J.J. / Winocour, P.D. / Leblond, L. / Siddiqui, M.A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2001 Title: Potent and selective bicyclic lactam inhibitors of thrombin. Part 4: transition state inhibitors. Authors: Bachand, B. / Tarazi, M. / St-Denis, Y. / Edmunds, J.J. / Winocour, P.D. / Leblond, L. / Siddiqui, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g37.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g37.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g37 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g37 | HTTPS FTP |
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-Related structure data
Related structure data | 1ihsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The molecule acts as a monomer |
-Components
#1: Protein | Mass: 33093.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: THROMBIN PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 1052.176 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-110 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 296K, temperature 296.0K |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 2, 1997 / Details: monochromator |
Radiation | Monochromator: graphite / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 24483 / Num. obs: 24483 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.196 / Num. unique all: 2197 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous with other thrombin complexes Starting model: PDB entry 1IHS Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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