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Yorodumi- PDB-1qur: HUMAN ALPHA-THROMBIN IN COMPLEX WITH BIVALENT, BENZAMIDINE-BASED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qur | |||||||||
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Title | HUMAN ALPHA-THROMBIN IN COMPLEX WITH BIVALENT, BENZAMIDINE-BASED SYNTHETIC INHIBITOR | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / TRYPSIN LIKE SERINE PROTEASE / BLOOD COAGULATION / 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 / 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) / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood microparticle / 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 / Resolution: 2 Å | |||||||||
Authors | Renatus, M. / Steinmetzer, T. | |||||||||
Citation | Journal: Eur.J.Biochem. / Year: 1999 Title: Design and evaluation of novel bivalent thrombin inhibitors based on amidinophenylalanines. Authors: Steinmetzer, T. / Renatus, M. / Kunzel, S. / Eichinger, A. / Bode, W. / Wikstrom, P. / Hauptmann, J. / Sturzebecher, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qur.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qur.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 1qur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qur_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 1qur_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 1qur_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1qur_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qur ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qur | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly of alpha-thrombin consists of the large and small subunit, linked by a disulfid bridge |
-Components
#1: Protein/peptide | Mass: 3188.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734 |
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#2: Protein | Mass: 29594.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734 |
#3: Protein/peptide | Mass: 2404.564 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The inhibitor was chemically synthesized AS COMBINATION OF ORGANIC AND SOLID PHASE PEPTIDE SYNTHESIS. THE ACTIVE SITE BINDING PORTION IS DERIVED FROM THE SYNTHETICAL INHIBITOR NAPAP,THE ...Details: The inhibitor was chemically synthesized AS COMBINATION OF ORGANIC AND SOLID PHASE PEPTIDE SYNTHESIS. THE ACTIVE SITE BINDING PORTION IS DERIVED FROM THE SYNTHETICAL INHIBITOR NAPAP,THE SEQUENCE OF THE EXOSITE BINDING PORTION WAS DERIVED FROM THE NATURALLY OCCURING INHIBITOR HIRUDIN, ISOLATED FROM THE MEDICAL LEECH AND THE SYNTHETICALLY SYNTHESIZED EXOSITE INHIBITOR MDL-28,050. |
#4: 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: 2.65 Å3/Da / Density % sol: 53.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: macro seeding Details: 100 mM Tris/HCl, 300-500 mM NaCl, 22-32% (w/v) PEG 8000, macro seeding, temperature 280K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→9 Å / Num. all: 54304 / Num. obs: 23412 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 21.604 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.2 / % possible all: 82 |
Reflection shell | *PLUS % possible obs: 82 % |
-Processing
Software |
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Refinement | Resolution: 2→9 Å / Data cutoff high rms absF: 10000 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Total num. of bins used: 22 /
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param / Topol file: CNS_TOPPAR:water_rep.param | ||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 9 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2085 / Rfactor Rfree: 0.2468 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.323 |