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Yorodumi- PDB-2ank: orally active thrombin inhibitors in complex with thrombin and an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ank | ||||||
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Title | orally active thrombin inhibitors in complex with thrombin and an exosite decapeptide | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / blood clotting / hydrolase / 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) Synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Lange, U.E.W. / Baucke, D. / Hornberger, W. / Mack, H. / Seitz, W. / Hoeffken, H.W. | ||||||
Citation | Journal: BIOORG.MED.CHEM.LETT. / Year: 2006 Title: Orally active thrombin inhibitors. Part 2: optimization of the P2-moiety Authors: Lange, U.E.W. / Baucke, D. / Hornberger, W. / Mack, H. / Seitz, W. / Hoeffken, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ank.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ank.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ank.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/2ank ftp://data.pdbj.org/pub/pdb/validation_reports/an/2ank | HTTPS FTP |
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-Related structure data
Related structure data | 2a2xC 2anmC 1nzqS C: citing same article (ref.) S: Starting model for refinement |
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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 | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 3848.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734 |
#3: Protein/peptide | |
#4: Chemical | ChemComp-N12 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS / Detector: CCD / Details: goebel mirror |
Radiation | Monochromator: goebel mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. all: 13596 / Num. obs: 12217 / % possible obs: 89.9 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.0803 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.44→2.53 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1170 / % possible all: 51.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NZQ Resolution: 2.46→44.13 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 111808.37 / Data cutoff high rms absF: 111808.37 / 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: 53.9508 Å2 / ksol: 0.354616 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.46→44.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.61 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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