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- PDB-1rtf: COMPLEX OF BENZAMIDINE WITH THE CATALYTIC DOMAIN OF HUMAN TWO CHA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rtf | ||||||
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Title | COMPLEX OF BENZAMIDINE WITH THE CATALYTIC DOMAIN OF HUMAN TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR [(TC)-T-PA] | ||||||
![]() | (TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR) x 2 | ||||||
![]() | SERINE PROTEASE / FIBRINOLYTIC ENZYMES | ||||||
Function / homology | ![]() t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis ...t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis / serine protease inhibitor complex / fibrinolysis / secretory granule / negative regulation of proteolysis / phosphoprotein binding / Schaffer collateral - CA1 synapse / protein modification process / blood coagulation / apical part of cell / response to hypoxia / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Bode, W. / Lamba, D. | ||||||
![]() | ![]() Title: The 2.3 A crystal structure of the catalytic domain of recombinant two-chain human tissue-type plasminogen activator Authors: Lamba, D. / Bauer, M. / Huber, R. / Fischer, S. / Rudolph, R. / Kohnert, U. / 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 | ![]() | 70.6 KB | Display | ![]() |
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PDB format | ![]() | 56 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 396 KB | Display | ![]() |
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Full document | ![]() | 397.9 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 10.3 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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Unit cell |
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Components
#1: Protein/peptide | Mass: 2121.343 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 28157.883 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-BEN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 12894 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. measured all: 65287 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.333 |
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Processing
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Refinement | Resolution: 2.3→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 31.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.64 |