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Yorodumi- PDB-1tq0: Crystal structure of the potent anticoagulant thrombin mutant W21... -
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-Basic information
Entry | Database: PDB / ID: 1tq0 | ||||||
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Title | Crystal structure of the potent anticoagulant thrombin mutant W215A/E217A in free form | ||||||
Components | (ProthrombinThrombin) x 2 | ||||||
Keywords | BLOOD CLOTTING / thrombin / anticoagulant | ||||||
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: 2.8 Å | ||||||
Authors | Pineda, A.O. / Chen, Z.-W. / Caccia, S. / Savvides, S.N. / Waksman, G. / Mathews, F.S. / Di Cera, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket Authors: Pineda, A.O. / Chen, Z.-W. / Caccia, S. / Cantwell, A.M. / Savvides, S.N. / Waksman, G. / Mathews, F.S. / 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 | 1tq0.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tq0.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tq0 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tq0 | HTTPS FTP |
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-Related structure data
Related structure data | 1tq7C 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3647.075 Da / Num. of mol.: 2 / Fragment: light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-pNUT / Cell line (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin #2: Protein | Mass: 29420.891 Da / Num. of mol.: 2 / Fragment: heavy chain / Mutation: W215A/E217A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-pNUT / Cell line (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin #3: 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: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 0.1 M CAPS, 0.2 M lithium sulfate, 0.12 M sodium dihydrogen phosphate, 0.53 M dipotassium hydrogen phosphate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 148 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 18776 / Num. obs: 18400 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 67.7 Å2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PPB Resolution: 2.8→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 822266.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.4796 Å2 / ksol: 0.322623 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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