+Open data
-Basic information
Entry | Database: PDB / ID: 1awh | ||||||
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Title | NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT | ||||||
Components | (ALPHA THROMBIN) x 2 | ||||||
Keywords | COMPLEX (PROTEASE/INHIBITOR) / PROTEINASE / BLOOD COAGULATION / TRYPSIN LIKE PROTEINASE / COMPLEX (PROTEASE-INHIBITOR) / COMPLEX (PROTEASE-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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Jhoti, H. / Cleasby, A. / Wonacott, A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Novel natural product 5,5-trans-lactone inhibitors of human alpha-thrombin: mechanism of action and structural studies. Authors: Weir, M.P. / Bethell, S.S. / Cleasby, A. / Campbell, C.J. / Dennis, R.J. / Dix, C.J. / Finch, H. / Jhoti, H. / Mooney, C.J. / Patel, S. / Tang, C.M. / Ward, M. / Wonacott, A.J. / Wharton, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1awh.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1awh.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 1awh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/1awh ftp://data.pdbj.org/pub/pdb/validation_reports/aw/1awh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THE DEPOSITED STRUCTURE IS THE DIMER FOUND IN THE ASYMMETRIC UNIT. |
-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACTIVE SITE INHIBITOR OF THROMBIN / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin #2: Protein | Mass: 29780.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACTIVE SITE INHIBITOR OF THROMBIN / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.69 % | ||||||||||||||||||||
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Crystal grow | pH: 4 / Details: 14% PEG4K, 100MM NA ACETATE, PH 4.0. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / PH range low: 5.5 / PH range high: 5 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 1, 1991 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Rsym value: 0.12 |
Reflection shell | Highest resolution: 3 Å |
Reflection | *PLUS Rmerge(I) obs: 0.124 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PPACK-THROMBIN Resolution: 3→10 Å / Rfactor Rwork: 0.202 / Rfactor obs: 0.202 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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