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Yorodumi- PDB-1c5v: STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c5v | ||||||
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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 cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER PLUS REFINEMENT / Resolution: 1.48 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 | 1c5v.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c5v.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 1c5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c5v_validation.pdf.gz | 415 KB | Display | wwPDB validaton report |
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Full document | 1c5v_full_validation.pdf.gz | 419.3 KB | Display | |
Data in XML | 1c5v_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 1c5v_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c5v ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c5v | HTTPS FTP |
-Related structure data
Related structure data | 1c5lC 1c5mC 1c5nC 1c5oC 1c5pC 1c5qC 1c5rC 1c5sC 1c5tC 1c5uC 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
#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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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-MG / |
#4: 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: 39.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.72 Details: trypsin-benzamidine, P3(1) 2 1 crystals 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 ...Details: trypsin-benzamidine, P3(1) 2 1 crystals 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 inhibitor-free solution of 1.84 M MgSO4 . 7 H2O, 150 mM Tris, 1 mM CaCl2, pH 7.72 over a period of several weeks with several replacements of the soaking solution. | ||||||||||||||||||||||||||||||
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: Feb 9, 1999 / 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→28.9 Å / Num. all: 22066 / % possible obs: 61 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.48→1.55 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 1.5 / % possible all: 33 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER PLUS REFINEMENT Resolution: 1.48→7.5 Å / Cross valid method: X-PLOR / σ(F): 2 Details: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT. RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: THR26, VAL31, GLN50, VAL53, LEU67, LYS87, ...Details: BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X-PLOR SCRIPT. RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: THR26, VAL31, GLN50, VAL53, LEU67, LYS87, MET104, SER110, SER170, LYS224, SER236. DISORDERED WATERS ARE: HOH262 WHICH IS CLOSE TO HOH308; HOH326 WHICH IS CLOSE TO HOH410; HOH382 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH384; HOH742 WHICH IS CLOSE TO HOH743; HOH921 WHICH IS CLOSE TO HOH1015; HOH350 WHICH IS CLOSE TO HOH466; HOH436 WHICH IS CLOSE TO HOH769 WHICH IS TO HOH1071; HOH444 WHICH IS CLOSE TO HOH452 AND TO A SYMMETRY-RELATED EQUIVALNET OF HOH454; HOH624 WHICH IS CLOSE TO HOH625; HOH368 WHICH IS CLOSE TO HOH1005; HOH997 WHICH IS CLOSE TO HOH998; HOH920 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; HOH1108 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; HOH1027 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; HOH1030 WHICH IS CLOSE TO HOH1031; HOH1070 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; HOH1071 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; HOH451 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH1013. HIS40 AND HIS91 IS MONOPROTONATED ON THE EPSILON NITROGEN. HIS57 IS MONOPROTONATED ON THE DELTA NITROGEN.
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Refinement step | Cycle: LAST / Resolution: 1.48→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.55 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): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.2 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.468 / % reflection Rfree: 10 % / Rfactor Rwork: 0.428 |