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Open data
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Basic information
Entry | Database: PDB / ID: 1j16 | ||||||
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Title | BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99/175/190RT | ||||||
![]() | Trypsin II, anionic | ||||||
![]() | HYDROLASE / SERINE PROTEASE / SERINE PROTEINASE | ||||||
Function / homology | ![]() Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsin / Neutrophil degranulation / digestion / collagen catabolic process / response to nutrient / serine-type endopeptidase activity / calcium ion binding ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsin / Neutrophil degranulation / digestion / collagen catabolic process / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stubbs, M.T. | ||||||
![]() | ![]() Title: Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-induced Structural Plasticity Authors: Reyda, S. / Sohn, C. / Klebe, G. / Rall, K. / Ullmann, D. / Jakubke, H.D. / Stubbs, M.T. #1: ![]() Title: pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design Authors: Stubbs, M.T. / Reyda, S. / Dullweber, F. / Moeller, M. / Klebe, G. / Dorsch, D. / Mederski, W.W.K.R. / Wurziger, H. #2: ![]() Title: Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinas Authors: Renatus, M. / Bode, W. / Huber, R. / Stuerzebecher, J. / Stubbs, M.T. #3: ![]() Title: Structural Aspects of Factor Xa Inhibition Authors: Stubbs, M.T. #4: ![]() Title: Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin Authors: Stubbs, M.T. / Huber, R. / 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 | ![]() | 64.2 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
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Full document | ![]() | 438.4 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
#1: Protein | Mass: 23836.756 Da / Num. of mol.: 1 / Mutation: K97E, L99Y, S190A, Y172S, P173S, G174F, K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BEN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2000 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→18.18 Å / Num. obs: 40861 |
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Processing
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Refinement | Resolution: 1.6→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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