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Yorodumi- PDB-1c5u: STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c5u | |||||||||
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Title | STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR | |||||||||
Components | PROTEIN (TRYPSIN) | |||||||||
Keywords | HYDROLASE / selective / S1 site inhibitor / structure-based drug design / urokinase / trypsin / thrombin | |||||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.37 Å | |||||||||
Authors | Katz, B.A. / Mackman, R. / Luong, C. / Radika, K. / Martelli, A. / Sprengeler, P.A. / Wang, J. / Chan, H. / Wong, L. | |||||||||
Citation | Journal: Chem.Biol. / Year: 2000 Title: Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator. Authors: Katz, B.A. / Mackman, R. / Luong, C. / Radika, K. / Martelli, A. / Sprengeler, P.A. / Wang, J. / Chan, H. / Wong, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c5u.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c5u.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c5u ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c5u | HTTPS FTP |
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-Related structure data
Related structure data | 1c5lC 1c5mC 1c5nC 1c5oC 1c5pC 1c5qC 1c5rC 1c5sC 1c5tC 1c5vC 1c5wC 1c5xC 1c5yC 1c5zC C: citing same article (ref.) |
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Similar structure data |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 214 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-ESP / | #6: 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: 2.04 Å3/Da / Density % sol: 18 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 5.5 Details: trypsin-benzamidine, P3(1) 2 1 were grown by vapor diffusion, as described for P2(1) 2(1) 2(1) (large cell) (Mangel, et al., Biochemistry 29, 8351-8357, 1990) The crystal was soaked in a ...Details: trypsin-benzamidine, P3(1) 2 1 were grown by vapor diffusion, as described for P2(1) 2(1) 2(1) (large cell) (Mangel, et al., Biochemistry 29, 8351-8357, 1990) The crystal was soaked in a solution of 1.73 M MgSO4 . 7 H2O, 150 mM MES, 1 mM CaCl2, 2.0 % DMSO,saturated with inhibitor, pH 5.50 over a period of several days with several replacements of the soaking solution., VAPOR DIFFUSION | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: batch method / Details: Katz, B.A., (1999) J. Mol. Biol., 292, 669. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 1998 / Details: MSC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→35.86 Å / Num. all: 33791 / % possible obs: 81 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.37→1.43 Å / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 2.2 / % possible all: 35.6 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT Resolution: 1.37→7.5 Å / Cross valid method: X-PLOR / σ(F): 1.8 Details: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Val31, Gln50, Val53, Leu67, Lys87, Ser88, ...Details: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Val31, Gln50, Val53, Leu67, Lys87, Ser88, Met104, Ser110, Ser170, Ser236, the non=amidine part of the inhibitor (246) Disordered waters are: HOH296 which is close to HOH326; HOH298 which is close to HOH311; HOH576 which is close to a symmetry-related equivalent of itself; HOH347 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH374 AND TO A SYMMETRY-RELATED EQUIVALENT OF HOH560. His91 is MONOPROTONATED ON THE EPSILON NITROGEN. His40 and HIS57 are DIPROTONATED.
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Refinement step | Cycle: LAST / Resolution: 1.37→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.43 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.5 Å / σ(F): 1.8 / % reflection Rfree: 10 % / Rfactor obs: 0.184 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.399 / % reflection Rfree: 10 % / Rfactor Rwork: 0.4 |