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Open data
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Basic information
Entry | Database: PDB / ID: 1bqy | ||||||
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Title | Plasminogen activator (TSV-PA) from snake venom | ||||||
![]() | PLASMINOGEN ACTIVATOR | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / FIBRINOLYSIS / PLASMINOGEN ACTIVATOR / SERINE PROTEINASE / SNAKE VENOM / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / BLOOD CLOTTING | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / toxin activity / serine-type endopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Parry, M.A.A. / Bode, W. | ||||||
![]() | ![]() Title: The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases. Authors: Parry, M.A. / Jacob, U. / Huber, R. / Wisner, A. / Bon, C. / Bode, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.8 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.7 KB | Display | ![]() |
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Full document | ![]() | 481 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ptbS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25634.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Organ: VENOM GLAND / Plasmid: PET / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETH | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.3 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 17988 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.444 / % possible all: 82.1 |
Reflection | *PLUS Num. measured all: 91942 |
Reflection shell | *PLUS % possible obs: 82.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PTB Resolution: 2.5→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rfactor Rwork: 0.352 |