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Yorodumi- PDB-1hai: THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hai | ||||||
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Title | THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO THROMBIN | ||||||
Components |
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Keywords | HYDROLASE/hydrolase inhibitor / SERINE PROTEINASE / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / lipopolysaccharide binding / Cell surface interactions at the vascular wall / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / response to wounding / platelet activation / Golgi lumen / positive regulation of protein localization to nucleus / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / G alpha (q) signalling events / positive regulation of cell growth / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / 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: 2.4 Å | ||||||
Authors | Tulinsky, A. / Vijayalakshmi, J. | ||||||
Citation | 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. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Hirudin-Thrombin Complex Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin Authors: Skrzypczak-Jankun, E. / Carperos, V.E. / Ravichandran, K.G. / Tulinsky, A. / Westbrook, M. / Maraganore, J.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS *B2* ON SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY AN EIGHT-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hai.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hai.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/1hai ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1hai | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO H 37 | |||||||||
Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / References: UniProt: P00734, thrombin |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / References: UniProt: P00734, thrombin |
#3: Chemical | ChemComp-0G6 / |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Compound details | THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. THREE-LETTER CODE 0G6 IS USED FOR PPACK |
Nonpolymer details | CHLOROMETHYLKETONE OF D-PHE-PRO-ARG-CHLOROMETHYLKETONE (PPACK) TERMINAL SUBCOMPONENT 0QE HAS ONLY ...CHLOROMETH |
Sequence details | CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT ...CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: microdialysis / Details: Bode, W., (1989) EMBO J., 8, 3467. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 13404 / % possible obs: 75 % / Rmerge(I) obs: 0.054 |
-Processing
Software |
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Refinement | Resolution: 2.4→7 Å / σ(F): 2 Details: THE REGIONS WITH INTERRUPTED ELECTRON DENSITIES ARE FOUND IN THE N-TERMINAL AND C-TERMINAL REGIONS OF A CHAIN, AND SOME RESIDUES IN THE AUTOLYSIS LOOP. THESE REGIONS INCLUDE: THR L 1H - GLU ...Details: THE REGIONS WITH INTERRUPTED ELECTRON DENSITIES ARE FOUND IN THE N-TERMINAL AND C-TERMINAL REGIONS OF A CHAIN, AND SOME RESIDUES IN THE AUTOLYSIS LOOP. THESE REGIONS INCLUDE: THR L 1H - GLU L 1C; ILE L 14K - ARG L 15; THR H 147 AND TRP H 148. RESIDUES THR H 149 - LYS H 149E IN THE GAMMA AUTOLYSIS LOOP ARE FOUND WITH NO ELECTRON DENSITIES AND ARE NOT INCLUDED IN THIS ENTRY. OTHER ATOMS WITH NO DENSITIES ARE GIVEN OCCUPANCY VALUES OF 0.01 IN THIS ENTRY.
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Refinement step | Cycle: LAST / Resolution: 2.4→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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