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Yorodumi- PDB-6oqj: SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH1/AA] AND PLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oqj | ||||||
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Title | SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH1/AA] AND PLASMINOGEN KRINGLE 2 | ||||||
Components |
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Keywords | PROTEIN BINDING / PLASMINOGEN BINDING PROTEIN / BLOOD CLOTTING | ||||||
Function / homology | Function and homology information plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / 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 / Schaffer collateral - CA1 synapse / kinase binding / 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 / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Streptococcus pyogenes (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Yuan, Y. / Castellino, F.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes. Authors: Yuan, Y. / Ayinuola, Y.A. / Singh, D. / Ayinuola, O. / Mayfield, J.A. / Quek, A. / Whisstock, J.C. / Law, R.H.P. / Lee, S.W. / Ploplis, V.A. / Castellino, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oqj.cif.gz | 430.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oqj.ent.gz | 359.8 KB | Display | PDB format |
PDBx/mmJSON format | 6oqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/6oqj ftp://data.pdbj.org/pub/pdb/validation_reports/oq/6oqj | HTTPS FTP |
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-Related structure data
Related structure data | 6okwC 6okxC 6okyC 6oq9C 6oqkC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10166.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9K / Production host: Komagataella pastoris (fungus) / References: UniProt: P00747*PLUS |
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#2: Protein | Mass: 6020.606 Da / Num. of mol.: 1 / Fragment: residues 85-134 / Mutation: R19A, H20A Source method: isolated from a genetically manipulated source Details: AP53 / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: pam, emm / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P49054 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement |
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NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |