+Open data
-Basic information
Entry | Database: PDB / ID: 3s7h | ||||||
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Title | Structure of thrombin mutant Y225P in the E* form | ||||||
Components | (Prothrombin) x 2 | ||||||
Keywords | HYDROLASE / serine protease | ||||||
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 / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / 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 / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Niu, W. / Chen, Z. / Gandhi, P. / Vogt, A. / Pozzi, N. / Pele, L.A. / Zapata, F. / Di Cera, E. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Crystallographic and Kinetic Evidence of Allostery in a Trypsin-like Protease. Authors: Niu, W. / Chen, Z. / Gandhi, P.S. / Vogt, A.D. / Pozzi, N. / Pelc, L.A. / Zapata, F. / Di Cera, E. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structural identification of the pathway of long-range communication in an allosteric enzyme. Authors: Gandhi, P.S. / Chen, Z. / 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 | 3s7h.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s7h.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 3s7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/3s7h ftp://data.pdbj.org/pub/pdb/validation_reports/s7/3s7h | HTTPS FTP |
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-Related structure data
Related structure data | 3qgnC 3s7kC 3beiS 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: 3995.430 Da / Num. of mol.: 1 / Fragment: Thrombin light chain / Mutation: Y225P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-modified pNUT / Organ (production host): kidney / References: UniProt: P00734, thrombin | ||
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#2: Protein | Mass: 29714.160 Da / Num. of mol.: 1 / Fragment: Thrombin heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-modified pNUT / Organ (production host): kidney / References: UniProt: P00734, thrombin | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Chemical | #5: 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: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Temperature: 295 K / pH: 8 Details: 0.1 M Tris and 8% PEG 8000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2010 |
Radiation | Monochromator: MIRROR+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: 1.9→40 Å / Num. obs: 30093 / % possible obs: 97.8 % / Observed criterion σ(I): -0.7 / Redundancy: 6.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.4 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BEI Resolution: 1.9→28.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.382 / SU ML: 0.083 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): -0.7 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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