+Open data
-Basic information
Entry | Database: PDB / ID: 1j14 | ||||||
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Title | BENZAMIDINE IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT | ||||||
Components | trypsin II, anionic | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Stubbs, M.T. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 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: Journal: Chembiochem / Year: 2002 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: Journal: J.MED.CHEM. / Year: 1998 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: Journal: Curr.Pharm.Des. / Year: 1996 Title: Structural Aspects of Factor Xa Inhibition Authors: Stubbs, M.T. #4: Journal: FEBS LETT. / Year: 1995 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j14.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j14.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 1j14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j14_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 1j14_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 1j14_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1j14_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/1j14 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/1j14 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23864.787 Da / Num. of mol.: 1 / Mutation: K97E, L99Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: pancreas / Plasmid: pyt / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.27 % |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 4, 1998 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.84 Å / Num. obs: 12713 |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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