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Yorodumi- PDB-1tbz: HUMAN THROMBIN WITH ACTIVE SITE N-METHYL-D PHENYLALANYL-N-[5-(AMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tbz | ||||||
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Title | HUMAN THROMBIN WITH ACTIVE SITE N-METHYL-D PHENYLALANYL-N-[5-(AMINOIMINOMETHYL)AMINO]-1-{{BENZOTHIAZOLYL)CARBONYL] BUTYL]-L-PROLINAMIDE TRIFLUROACETATE AND EXOSITE-HIRUGEN | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) / 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 / serine-type endopeptidase inhibitor 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) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Matthews, J.H. / Krishnan, R. / Costanzo, M.J. / Maryanoff, B.E. / Tulinsky, A. | ||||||
Citation | Journal: Biophys.J. / Year: 1996 Title: Crystal structures of thrombin with thiazole-containing inhibitors: probes of the S1' binding site. Authors: Matthews, J.H. / Krishnan, R. / Costanzo, M.J. / Maryanoff, B.E. / Tulinsky, A. #1: Journal: Protein Sci. / Year: 1994 Title: The Isomorphous Structures of Prethrombin2, Hirugen-, and Ppack-Thrombin: Changes Accompanying Activation and Exosite Binding to Thrombin Authors: Vijayalakshmi, J. / Padmanabhan, K.P. / Mann, K.G. / Tulinsky, A. #2: Journal: Blood Coagulation Fibrinolysis / Year: 1993 Title: Active Site and Exosite Binding of Alpha-Thrombin Authors: Tulinsky, A. / Qiu, X. #3: Journal: Biochemistry / Year: 1992 Title: Structure of the Hirulog 3-Thrombin Complex and Nature of the S' Subsites of Substrates and Inhibitors Authors: Qiu, X. / Padmanabhan, K.P. / Carperos, V.E. / Tulinsky, A. / Kline, T. / Maraganore, J.M. / Fenton II, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tbz.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tbz.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 1tbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/1tbz ftp://data.pdbj.org/pub/pdb/validation_reports/tb/1tbz | HTTPS FTP |
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-Related structure data
Related structure data | 1a4wC 1fpcS 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/peptide , 2 types, 2 molecules LI
#1: Protein/peptide | Mass: 4096.534 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 / Source method: isolated from a natural source / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945 |
-Protein , 1 types, 1 molecules H
#2: Protein | Mass: 29780.219 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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-Non-polymers , 3 types, 126 molecules
#4: Chemical | ChemComp-00Q / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER |
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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: 2.4 Å3/Da / Density % sol: 51 % | |||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop - macroseeding / pH: 7.3 Details: 0.1M PHOSPHATE BUFFER AT PH 7.3, 27-28% PEG 8000. HANGING DROPS AND MACROSEEDING ., vapor diffusion - hanging drop - macroseeding | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. obs: 15300 / % possible obs: 75 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 50 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FPC Resolution: 2.3→7 Å / σ(F): 2
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |