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Yorodumi- PDB-3oy5: The crystal structure of uPA complex with peptide inhibitor MH027... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oy5 | ||||||
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Title | The crystal structure of uPA complex with peptide inhibitor MH027 at pH7.4 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / UROKINASE-TYPE PLASMINOGEN ACTIVATOR / PEPTIDYL INHIBITOR / PHARMACOPHORE / HYDROLASE / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Jiang, L.G. / Andreasen, P.A. / Huang, M.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The binding mechanism of a peptidic cyclic serine protease inhibitor Authors: Jiang, L.G. / Svane, A.S.P. / Sorensen, H.P. / Jensen, J.K. / Hosseini, M. / Chen, Z. / Weydert, C. / Nielsen, J.T. / Christensen, A. / Yuan, C. / Jensen, K.J. / Nielsen, N.C. / Malmendal, A. ...Authors: Jiang, L.G. / Svane, A.S.P. / Sorensen, H.P. / Jensen, J.K. / Hosseini, M. / Chen, Z. / Weydert, C. / Nielsen, J.T. / Christensen, A. / Yuan, C. / Jensen, K.J. / Nielsen, N.C. / Malmendal, A. / Huang, M.D. / Andreasen, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oy5.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oy5.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oy5_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 3oy5_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 3oy5_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3oy5_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/3oy5 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/3oy5 | HTTPS FTP |
-Related structure data
Related structure data | 3ox7C 3oy6C 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: 28442.373 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, UNP residues 179-431 / Mutation: C122A, N145Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: P00749, u-plasminogen activator |
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#2: Protein/peptide | Mass: 2254.508 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC |
#3: Chemical | ChemComp-SO4 / |
#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: 1.98 Å3/Da / Density % sol: 38.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100mM Tris-Hcl, 2.0M (NH4)2SO4, 0.05% NAN3, 5% PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→60 Å / Num. all: 10343 / Num. obs: 10343 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.079 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2.31→2.35 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 14.4 / Rsym value: 0.142 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NWN Resolution: 2.31→34.94 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.603 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.614 / ESU R Free: 0.256 / 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: 13.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→34.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.311→2.371 Å / Total num. of bins used: 20
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