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Yorodumi- PDB-2thf: STRUCTURE OF HUMAN ALPHA-THROMBIN Y225F MUTANT BOUND TO D-PHE-PRO... -
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-Basic information
Entry | Database: PDB / ID: 2thf | ||||||
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Title | STRUCTURE OF HUMAN ALPHA-THROMBIN Y225F MUTANT BOUND TO D-PHE-PRO-ARG-CHLOROMETHYLKETONE | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Caccia, S. / Futterer, K. / Di Cera, E. / Waksman, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Unexpected crucial role of residue 225 in serine proteases. Authors: Guinto, E.R. / Caccia, S. / Rose, T. / Futterer, K. / Waksman, G. / Di Cera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2thf.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2thf.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2thf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/2thf ftp://data.pdbj.org/pub/pdb/validation_reports/th/2thf | HTTPS FTP |
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-Related structure data
Related structure data | 1b7xC 1thpC 1ppbS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734 |
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#2: Protein | Mass: 29764.219 Da / Num. of mol.: 1 / Mutation: Y225F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Cell line (production host): BABY HAMSTER KIDNEY CELLS (BHK-21) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00734, thrombin |
#3: Chemical | ChemComp-0G6 / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | D-PHE-PRO-ARG-CHLOROMETHYLKETONE HAS FORMED TWO COVALENT CONNECTIONS TO THROMBIN: 1) VIA A ...D-PHE-PRO-ARG-CHLOROMETH |
Sequence details | THE PROTEIN USED IN THE PRESENT STRUCTURE DETERMINATION COMPRISED AMINO ACIDS 1H TO 247 ...THE PROTEIN USED IN THE PRESENT STRUCTURE DETERMINAT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusionDetails: mutants are inhibited by a 10-fold molar excess of H-D-Phe-Pro-Arg-chloromethylketone for 30 min at room temperature PH range low: 6.5 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03 |
Detector | Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 18509 / % possible obs: 94.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.131 / % possible all: 89.6 |
Reflection | *PLUS Num. measured all: 68774 |
Reflection shell | *PLUS % possible obs: 89.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPB Resolution: 2.1→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.24 |