+Open data
-Basic information
Entry | Database: PDB / ID: 1f5k | |||||||||
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Title | UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN-BENZAMIDINE COMPLEX | |||||||||
Components | UROKINASE-TYPE PLASMINOGEN ACTIVATORUrokinase | |||||||||
Keywords | HYDROLASE / UROKINASE / INHIBITOR / SERINE PROTEASE / HUMAN | |||||||||
Function / homology | Function and homology information u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Zeslawska, E. / Schweinitz, A. / Karcher, A. / Sondermann, P. / Sperl, S. / Sturzebecher, J. / Jacob, U. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystals of the urokinase type plasminogen activator variant beta(c)-uPAin complex with small molecule inhibitors open the way towards structure-based drug design. Authors: Zeslawska, E. / Schweinitz, A. / Karcher, A. / Sondermann, P. / Sperl, S. / Sturzebecher, J. / Jacob, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f5k.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f5k.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 1f5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f5k ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f5k | HTTPS FTP |
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-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: 28444.346 Da / Num. of mol.: 1 / Fragment: B CHAIN / Mutation: C279S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) References: GenBank: 1199928, UniProt: P00749*PLUS, u-plasminogen activator | ||||
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#2: Chemical | #3: Chemical | ChemComp-BEN / | #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: 2.1 Å3/Da / Density % sol: 41.42 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||
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 / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→500 Å / Num. obs: 19239 / % possible obs: 83.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.107 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 74.9 |
Reflection | *PLUS Lowest resolution: 500 Å |
Reflection shell | *PLUS % possible obs: 74.9 % |
-Processing
Software |
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Refinement | Resolution: 1.8→500 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.204 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |