+Open data
-Basic information
Entry | Database: PDB / ID: 8asf | ||||||
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Title | Crystal structure of Thrombin in complex with macrocycle T1 | ||||||
Components |
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Keywords | HYDROLASE / Serine endopeptidases / alpha-thrombin / activated factor IIa / fibrinogenase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Chinellato, M. / Angelini, A. / Nielsen, A. / Heinis, C. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3 Authors: Nielsen, A. / Chinellato, M. / Cendron, L. / Angelini, A. / Heinis, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8asf.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8asf.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 8asf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/8asf ftp://data.pdbj.org/pub/pdb/validation_reports/as/8asf | HTTPS FTP |
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-Related structure data
Related structure data | 8aseC 6z48S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: missing residues are not visible in the electron density maps Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Homo sapiens (human) / References: UniProt: P00734, thrombin #2: Protein | Mass: 29780.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: missing residues are not visible in the electron density maps Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Homo sapiens (human) / References: UniProt: P00734, thrombin #3: Chemical | Mass: 635.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H35ClN4O4S3 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100 mM sodium acetate, 50 mM magnesium chloride hexahydrate, 8% w/v PEG 3350, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→38.09 Å / Num. obs: 20556 / % possible obs: 86.9 % / Redundancy: 3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.58→2.67 Å / Num. unique obs: 20556 / CC1/2: 0.885 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z48 Resolution: 2.58→38.06 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 119.52 Å2 / Biso mean: 41.458 Å2 / Biso min: 19.47 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→38.06 Å
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