+Open data
-Basic information
Entry | Database: PDB / ID: 3biu | ||||||
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Title | Human thrombin-in complex with UB-THR10 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease-inhibitor complex / Blood Clotting / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Secreted / Zymogen / 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 / 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 / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / 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) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Gerlach, C. / Smolinski, M. / Steuber, H. / Sotriffer, C.A. / Heine, A. / Hangauer, D.G. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007 Title: Thermodynamic Inhibition Profile of a Cyclopentyl and a Cyclohexyl Derivative towards Thrombin: The Same but for Different Reasons Authors: Gerlach, C. / Smolinski, M. / Steuber, H. / Sotriffer, C.A. / Heine, A. / Hangauer, D.G. / Klebe, G. #1: Journal: to be published Title: Privileged structures for serine proteases Docking and direct design in the protein binding pocket Authors: Gerlach, C. / Smolinski, M. / Steuber, H. / Sotriffer, C.A. / Heine, A. / Hangauer, D.G. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3biu.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3biu.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 3biu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3biu_validation.pdf.gz | 773.9 KB | Display | wwPDB validaton report |
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Full document | 3biu_full_validation.pdf.gz | 780.7 KB | Display | |
Data in XML | 3biu_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3biu_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3biu ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3biu | HTTPS FTP |
-Related structure data
Related structure data | 3bivC 1k22S 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 on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 2 molecules LI
#1: Protein/peptide | Mass: 3432.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Plasma / References: UniProt: P00734, thrombin |
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#3: Protein/peptide | Mass: 1534.554 Da / Num. of mol.: 1 / Fragment: Residues in database 60-71 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945 |
-Protein / Sugars , 2 types, 2 molecules H
#2: Protein | Mass: 29594.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Plasma / References: UniProt: P00734, thrombin |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 166 molecules
#5: Chemical | #6: Chemical | ChemComp-10U / ( | #7: 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: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 15332 / Num. obs: 15332 / % possible obs: 96.9 % / Redundancy: 3.4 % / Rsym value: 0.067 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 786 / Rsym value: 0.225 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K22 Resolution: 2.3→10 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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