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Yorodumi- PDB-2bvr: Human thrombin complexed with fragment-based small molecules occu... -
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-Basic information
Entry | Database: PDB / ID: 2bvr | ||||||
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Title | Human thrombin complexed with fragment-based small molecules occupying the S1 pocket | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / 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 / 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 / SYNCHROTRON / OTHER / Resolution: 1.25 Å | ||||||
Authors | Neumann, T. / Junker, H.-D. / Keil, O. / Burkert, K. / Ottleben, H. / Gamer, J. / Sekul, R. / Deppe, H. / Feurer, A. / Tomandl, D. / Metz, G. | ||||||
Citation | Journal: Lett.Drug Des.Discovery / Year: 2005 Title: Discovery of Thrombin Inhibitor Fragments from Chemical Microarray Screening Authors: Neumann, T. / Junker, H.-D. / Keil, O. / Burkert, K. / Ottleben, H. / Gamer, J. / Sekul, R. / Deppe, H. / Feurer, A. / Tomandl, D. / Metz, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bvr.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bvr.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bvr_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 2bvr_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 2bvr_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 2bvr_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bvr ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bvr | HTTPS FTP |
-Related 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: 29050.443 Da / Num. of mol.: 1 / Fragment: LARGE SUBUNIT, RESIDUES 364-622 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 1378.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P09945 |
#3: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: SMALL SUBUNIT, RESIDUES 328-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00734, thrombin |
#4: Chemical | ChemComp-4CP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 0.9791 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→15 Å / Num. obs: 97319 / % possible obs: 99.6 % / Observed criterion σ(I): 5.9 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: CNX / Version: 2002 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.25→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 55.77 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.25→15 Å
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Refine LS restraints |
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Xplor file |
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