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Yorodumi- PDB-4jk6: Human urokinase-type Plasminogen Activator (uPA) in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jk6 | ||||||
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Title | Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Aba) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease / chymotrypsin fold / urokinase-type plasminogen activator / bicyclic peptide inhibitor / D-amino acids / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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) Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Buth, S.A. / Leiman, P.G. / Chen, S. / Heinis, C. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Improving binding affinity and stability of Peptide ligands by substituting glycines with d-amino acids. Authors: Chen, S. / Gfeller, D. / Buth, S.A. / Michielin, O. / Leiman, P.G. / Heinis, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jk6.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jk6.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jk6_validation.pdf.gz | 975.8 KB | Display | wwPDB validaton report |
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Full document | 4jk6_full_validation.pdf.gz | 978.1 KB | Display | |
Data in XML | 4jk6_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4jk6_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/4jk6 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/4jk6 | HTTPS FTP |
-Related structure data
Related structure data | 4jk5C 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 27586.420 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: C299A, N322Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: 9606 / Gene: PLAU / Plasmid: pSecTagA / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: P00749, u-plasminogen activator |
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#2: Protein/peptide | |
-Non-polymers , 5 types, 117 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-P6G / | #6: Chemical | ChemComp-ZBR / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 50mM Na3(cit) pH 4.9, 5% v/v PEG400, 1.8M (NH4)2SO4, 0.05% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2012 / Details: mirrors |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry and a toroidal mirror (M2) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.16 Å / Num. all: 11881 / Num. obs: 11879 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.048 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1037 / Rsym value: 0.308 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NWN Resolution: 2.2→33.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 11.095 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.204 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.333 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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