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Yorodumi- PDB-1b2i: KRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF ... -
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-Basic information
Entry | Database: PDB / ID: 1b2i | ||||||
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Title | KRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID (AMCHA) COMPLEX | ||||||
Components | PROTEIN (PLASMINOGEN) | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / FIBRINOLYSIS / LYSINE-BINDING DOMAIN / PLASMINOGEN / KRINGLE 2 | ||||||
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 / 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) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, DYNAMIC SIMULATED ANNEALING | ||||||
Authors | Marti, D.N. / Schaller, J. / Llinas, M. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Solution structure and dynamics of the plasminogen kringle 2-AMCHA complex: 3(1)-helix in homologous domains. Authors: Marti, D.N. / Schaller, J. / Llinas, M. #1: Journal: Biochemistry / Year: 1997 Title: Ligand Preferences of Kringle 2 and Homologous Domains of Human Plasminogen: Canvassing Weak, Intermediate and High-Affinity Binding Sites by 1H-NMR Authors: Marti, D.N. / Hu, C.K. / An, S.S.A. / Von Haller, P. / Schaller, J. / Llinas, M. #2: Journal: Biochemistry / Year: 1996 Title: Recombinant Gene Expression and 1H NMR Characteristics of the Kringle (2+3) Supermodule: Spectroscopic/Functional Individuality of Plasminogen Kringle Domains Authors: Soehndel, S. / Hu, C.K. / Marti, D. / Affolter, M. / Schaller, J. / Llinas, M. / Rickli, E.E. #3: Journal: Eur.J.Biochem. / Year: 1994 Title: Expression, Purification and Characterization of the Recombinant Kringle 2 and Kringle 3 Domains of Human Plasminogen and Analysis of Their Binding Affinity for Omega-Aminocarboxylic Acids Authors: Marti, D. / Schaller, J. / Ochensberger, B. / Rickli, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b2i.cif.gz | 515.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b2i.ent.gz | 430.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2i ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2i | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9651.812 Da / Num. of mol.: 1 / Fragment: KRINGLE 2 DOMAIN / Mutation: C181T, E182S, C188G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE-8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00747, plasmin |
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#2: Chemical | ChemComp-AMH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: SEE PAPER / pH: 5.1 / Pressure: AMBIENT / Temperature: 310 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, DYNAMIC SIMULATED ANNEALING / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: TOTAL ENERGY, RAMACHANDRAN PLOT, LEAST RESTRAINT VIOLATION Conformers calculated total number: 150 / Conformers submitted total number: 20 |