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Yorodumi- PDB-3mhw: The complex crystal Structure of Urokianse and 2-Aminobenzothiazole -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mhw | ||||||
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Title | The complex crystal Structure of Urokianse and 2-Aminobenzothiazole | ||||||
Components | Urokinase-type plasminogen activator | ||||||
Keywords | HYDROLASE / Blood coagulation / Fibrinolysis / Plasminogen activation | ||||||
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 / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Jiang, L.-G. / Yuan, C. / Chen, L.-Q. / Huang, M.-D. | ||||||
Citation | Journal: CHIN.J.STRUCT.CHEM. / Year: 2009 Title: Crystal Structures of 2-Aminobenzothiazole-based Inhibitors in Complexes with Urokinase-type Plasminogen Activator Authors: Jiang, L.-G. / Yu, H.-Y. / Yuan, C. / Wang, J.-D. / Chen, L.-Q. / Meehan, E.J. / Huang, Z.-X. / Huang, M.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mhw.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mhw.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mhw_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 3mhw_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 3mhw_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3mhw_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mhw ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mhw | HTTPS FTP |
-Related structure data
Related structure data | 3kidC 2nwnS S: Starting model for refinement 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
#1: Protein | Mass: 27846.688 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 179-425 / Mutation: C122S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Human / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P00749, u-plasminogen activator | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-ABV / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | 2-AMINOBENZOSequence details | THE PDB IS NUMBERED BY CHYMOTRYPS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.05M sodium citrate, 1.95M (NH4)2SO4, 0.05% NaN3, 5% PEG 400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2009 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→60 Å / Num. all: 38364 / Num. obs: 47327 / % possible obs: 91.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.079 / Rsym value: 0.055 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.45→1.52 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2 / Num. unique all: 4814 / Rsym value: 0.49 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NWN Resolution: 1.45→35.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.147 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.991 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→35.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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