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- PDB-1a0h: THE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1a0h | |||||||||
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Title | THE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE/THROMBIN AND CARBOHYDRATE/KRINGLE/THROMBIN INTERACTIONS AND LOCATION OF THE LINKER CHAIN | |||||||||
![]() | (MEIZOTHROMBIN) x 2 | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / COAGULATION / THROMBIN / PROTHROMBIN / MEIZOTHROMBIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Martin, P.D. / Malkowski, M.G. / Box, J. / Esmon, C.T. / Edwards, B.F.P. | |||||||||
![]() | ![]() Title: New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK. Authors: Martin, P.D. / Malkowski, M.G. / Box, J. / Esmon, C.T. / Edwards, B.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.4 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 54.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.90024, -0.43536, -0.00555), Vector: |
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Components
#1: Protein | Mass: 17868.338 Da / Num. of mol.: 2 / Fragment: F2/THROMBIN DOMAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 29772.422 Da / Num. of mol.: 2 / Fragment: F2/THROMBIN DOMAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETH | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.4 Å3/Da / Density % sol: 76 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 17 MG/ML PROTEIN, 2% PEG4000, .25 M AMMONIUM PHOSPHATE, PH 8.0, 33% SATURATED AMMONIUM SULFATE | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1996 / Details: 0.3 MM COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→42.3 Å / Num. obs: 31648 / % possible obs: 88 % / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.2→3.3 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.19 / % possible all: 60 |
Reflection shell | *PLUS % possible obs: 60 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: THROMBIN Resolution: 3.2→7 Å / Data cutoff high absF: 99999999 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 3.2→7 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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