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Open data
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Basic information
Entry | Database: PDB / ID: 1ql7 | ||||||
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Title | FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN | ||||||
![]() | TRYPSIN | ||||||
![]() | SERINE PROTEASE / HYDROLASE / SERINE PROTEINASE | ||||||
Function / homology | ![]() trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Stubbs, M.T. | ||||||
![]() | ![]() Title: Ph-Dependent Binding Modes Observed in Trypsin Crystals: Lessons for the 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. #1: 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 Urokinase Authors: Renatus, M. / Bode, W. / Huber, R. / Stuerzebecher, J. / Stubbs, M.T. #2: ![]() Title: Structural Aspects of Factor Xa Inhibition Authors: Stubbs, M.T. #3: ![]() 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 | ![]() | 53.5 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.7 KB | Display | ![]() |
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Full document | ![]() | 476.9 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 10 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
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ZEN / [ |
#5: Water | ChemComp-HOH / |
Compound details | THE 223 AMINO ACIDS OF BOVINE TRYPSIN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS ...THE 223 AMINO ACIDS OF BOVINE TRYPSIN ARE IDENTIFIED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 0.1M IMIDAZOLE PH8.0, 0.1M AMMONIUM SULPHATE, 20% PEG8K, pH 8.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / pH: 8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MIRRORS |
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→100 Å / Num. obs: 13570 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.425 / Rsym value: 0.425 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.1→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
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Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.14 Å / Total num. of bins used: 20
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.203 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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