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Yorodumi- PDB-1h8d: X-ray structure of the human alpha-thrombin complex with a tripep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h8d | ||||||
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Title | X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate inhibitor. | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of serine-type peptidase activity / 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 ...negative regulation of serine-type peptidase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Skordalakes, E. / Dodson, G.G. / Green, D. / Deadman, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Inhibition of Human Alpha-Thrombin by a Phosphonate Tripeptide Proceeds Via a Metastable Pentacoordinated Phosphorus Intermediate Authors: Skordalakes, E. / Dodson, G.G. / Green, D.S. / Goodwin, C.A. / Scully, M.F. / Hudson, H.R. / Kakkar, V.V. / Deadman, J.J. #1: Journal: Biochemistry / Year: 1996 Title: Inhibition of Trypsin and Thrombin by Amino (4-Amidinophenyl)Methanephosphonate Diphenyl Ester Derivatives: X-Ray and Molecular Models Authors: Bertrand, J.A. / Oleksyszyn, J. / Kam, C.M. / Boduszek, B. / Presnell, S. / Plaskon, R.R. / Suddath, F.L. / Powers, J.C. / Williams, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8d.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8d.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8d ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8d | HTTPS FTP |
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-Related structure data
Related structure data | 1h8iC 1hgtS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29797.395 Da / Num. of mol.: 1 / Fragment: THROMBIN HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 1363.399 Da / Num. of mol.: 1 / Fragment: RESIDUES 55 TO 64 / Source method: isolated from a natural source / Source: (natural) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P01050 |
#3: Protein/peptide | Mass: 3404.819 Da / Num. of mol.: 1 / Fragment: THROMBIN LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin |
#4: Chemical | ChemComp-PHW / |
#5: 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: 2.59 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: 20% PEG 8K, 0.05MM NAHPO4, 0.1M NACL, PH 7.20 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 / Method: vapor diffusion, hanging dropDetails: Skordalakes, E., (1997) J. Am. Chem. Soc., 119, 9935. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Date: Jun 7, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→15 Å / Num. obs: 68615 / % possible obs: 95.4 % / Observed criterion σ(I): 5 / Redundancy: 3 % / Biso Wilson estimate: 16.27 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.056 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 6 / Rsym value: 0.131 / % possible all: 96.6 |
Reflection | *PLUS Lowest resolution: 8 Å / Num. obs: 66600 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HGT Resolution: 1.4→14 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 18.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→14 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.175 / Rfactor Rfree: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |