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Yorodumi- PDB-1bui: Structure of the ternary microplasmin-staphylokinase-microplasmin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bui | ||||||
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Title | Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PLASMIN / STAPHYLOKINASE / SERINE PROTEINASE / FIBRINOLYSIS / COFACTOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / plasminogen activation / Activation of Matrix Metalloproteinases / apolipoprotein binding / : / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / kinase binding / Schaffer collateral - CA1 synapse / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / endopeptidase activity / protease binding / collagen-containing extracellular matrix / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Staphylococcus phage 42D.m (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Parry, M.A.A. / Fernandez-Catalan, C. / Bergner, A. / Huber, R. / Hopfner, K. / Schlott, B. / Guehrs, K. / Bode, W. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action. Authors: Parry, M.A. / Fernandez-Catalan, C. / Bergner, A. / Huber, R. / Hopfner, K.P. / Schlott, B. / Guhrs, K.H. / Bode, W. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: DSSP | ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bui.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bui.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1bui ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1bui | 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: 27335.402 Da / Num. of mol.: 2 / Fragment: Peptidase S1 catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Escherichia coli (E. coli) / References: UniProt: P00747, plasmin #2: Protein | | Mass: 14598.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 42D.m (virus) / Genus: Lambda-like viruses / References: UniProt: P15240 #3: Chemical | ChemComp-0GJ / | #4: Water | ChemComp-HOH / | Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETH | |
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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: 3.42 Å3/Da / Density % sol: 67 % | |||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→10 Å / Num. obs: 28745 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.075 |
Reflection | *PLUS Num. measured all: 483198 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1FAX AND 2SAK Resolution: 2.65→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.65→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |