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Yorodumi- PDB-1hag: THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THR... -
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-Basic information
Entry | Database: PDB / ID: 1hag | ||||||
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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 / COMPLEX(SERINE PROTEINASE-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 / 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 / serine-type endopeptidase inhibitor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / positive regulation of cell growth / regulation of cell shape / 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 / positive regulation of cell population proliferation / calcium ion binding / 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 / Resolution: 2 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 | 1hag.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hag.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hag_validation.pdf.gz | 403 KB | Display | wwPDB validaton report |
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Full document | 1hag_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 1hag_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1hag_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/1hag ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1hag | HTTPS FTP |
-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 E 37 2: RESIDUE TYR I 63 IN THE HIRUGEN MOLECULE IS BONDED TO THE SULFATO-TYROSINE. | ||||||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33858.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 1363.399 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P28505 |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Compound details | PEPTIDE ASP I 55 - LEU 64 AT THE EXOSITE IS HIRUGEN MOLECULE, WHICH IS PART OF HIRUDIN 53 - 65. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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 Å / Lowest resolution: 15 Å / Num. obs: 16642 / % possible obs: 66 % / Observed criterion σ(F): 1 / Num. measured all: 23973 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.3 Å / % possible obs: 43 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 3 Details: FLEXIBLE REGIONS WITH RELATIVELY HIGH TEMPERATURE FACTORS ARE FOUND IN THE ACTIVATION DOMAIN, N-TERMINAL AND C-TERMINAL REGIONS. THESE REGIONS INCLUDE: THR E 1H - GLU E 1C, GLU E 14H - GLUE ...Details: FLEXIBLE REGIONS WITH RELATIVELY HIGH TEMPERATURE FACTORS ARE FOUND IN THE ACTIVATION DOMAIN, N-TERMINAL AND C-TERMINAL REGIONS. THESE REGIONS INCLUDE: THR E 1H - GLU E 1C, GLU E 14H - GLUE 18, GLU E 146 - GLN E 151 (GAMMA AUTOLYSIS LOOP), PRO E 186 - ARG E 187, GLY E 219 - GLY E 223, AND ASP E 243 - GLU E 247. A FEW ATOMS IN THE AUTOLYSIS LOOP (N THR E 147, CA TRP E 148, CB TRP E 148, AND THE SIDE CHAIN OF THRE 149) DO NOT HAVE WELL-DEFINED ELECTRON DENSITY. ATOMS WITH NO ELECTRON DENSITIES ARE GIVEN OCCUPANCIES OF 0.01 IN THE ENTRY.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR/PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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