+Open data
-Basic information
Entry | Database: PDB / ID: 4rko | ||||||
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Title | Crystal structure of thrombin mutant S195T bound with PPACK | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Trypsin-like proteases / catalysis / allosteric regulation / 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 / 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 / positive regulation of cell growth / regulation of cell shape / 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 / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Pelc, A.L. / Chen, Z. / Gohara, D.W. / Vogt, A.D. / Pozzi, N. / Di Cera, E. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Why ser and not thr brokers catalysis in the trypsin fold. Authors: Pelc, L.A. / Chen, Z. / Gohara, D.W. / Vogt, A.D. / Pozzi, N. / Di Cera, E. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Molecular dissection of Na+ binding to thrombin. Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / 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 | 4rko.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rko.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rko_validation.pdf.gz | 828.3 KB | Display | wwPDB validaton report |
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Full document | 4rko_full_validation.pdf.gz | 834.8 KB | Display | |
Data in XML | 4rko_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 4rko_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/4rko ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rko | HTTPS FTP |
-Related structure data
Related structure data | 4rkjC 1shhS 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
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules BA
#1: Protein | Mass: 29794.246 Da / Num. of mol.: 1 / Mutation: S195T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 4860.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 150 molecules
#3: Chemical | ChemComp-0G6 / | ||||
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#4: Chemical | ChemComp-MES / | ||||
#5: Chemical | #6: Chemical | ChemComp-NA / | #8: 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: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, pH 6.5, 15% PEG 6000 and 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.84→40 Å / Num. all: 24760 / Num. obs: 22779 / % possible obs: 92 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1SHH Resolution: 1.84→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.221 / SU ML: 0.118 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.153 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.172 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.844→1.892 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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