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- PDB-1i5k: STRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 D... -
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Basic information
Entry | Database: PDB / ID: 1i5k | ||||||
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Title | STRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 DOMAIN OF HUMAN PLASMINOGEN TO AN INTERNAL PEPTIDE FROM A GROUP A STREPTOCOCCAL SURFACE PROTEIN | ||||||
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![]() | BLOOD CLOTTING / Human Plasminogen Kringle-2 / Kringles / VEK-30 | ||||||
Function / homology | ![]() plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / 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 / protein antigen binding / tissue regeneration / 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 / 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 / protease binding / endopeptidase activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rios-Steiner, J.L. / Schenone, M. / Mochalkin, I. / Tulinsky, A. / Castellino, F.J. | ||||||
![]() | ![]() Title: Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein. Authors: Rios-Steiner, J.L. / Schenone, M. / Mochalkin, I. / Tulinsky, A. / Castellino, F.J. #1: ![]() Title: Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen. Authors: Chang, Y. / Mochalkin, I. / McCance, S.G. / Cheng, B. / Tulinsky, A. / Castellino, F.J. #2: ![]() Title: The refined structure of the epsilon-aminocaproic acid complex of human plasminogen kringle 4. Authors: Wu, T.P. / Padmanabhan, K. / Tulinsky, A. / Mulichak, A.M. #3: ![]() Title: Kringle 2 mediates high affinity binding of plasminogen to an internal sequence in streptococcal surface protein PAM. Authors: Wistedt, A.C. / Kotarsky, H. / Marti, D. / Ringdahl, U. / Castellino, F.J. / Schaller, J. / Sjobring, U. #4: ![]() Title: Enhancement trough mutagenesis of the binding of the isolated kringle 2 domain of human plasminogen to omega-amino acid ligands and to an internal sequence of a Streptococcal surface protein. Authors: Nilsen, S.L. / Prorok, M. / Castellino, F.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.3 KB | Display | ![]() |
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Full document | ![]() | 401.3 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pk4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The assembly in the assymetric unit constitutes a dimer of the monomeric complex of a Kringle-2:vek30 complex. |
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Components
#1: Protein | Mass: 9774.923 Da / Num. of mol.: 2 / Fragment: MODIFIED RECOMBINANT KRINGLE-2 DOMAIN / Mutation: C4G/E56D/L72Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein/peptide | Mass: 3635.021 Da / Num. of mol.: 2 / Fragment: VEK-30 (30 RESIDUE INTERNAL PEPTIDE) / Source method: obtained synthetically Details: VEK-30 was synthesized by automated solid phase peptide synthesis References: UniProt: P49054 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 23%(w/v) PEG 3350, 0.1 M Mes, 0.2 M Li2SO4, 2mM CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2000 |
Radiation | Monochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.039 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 74852 / Num. obs: 73280 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11063 / % possible all: 84.3 |
Reflection | *PLUS Num. obs: 11063 / Num. measured all: 74852 |
Reflection shell | *PLUS % possible obs: 84.3 % / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Using K4 Pg (PDB entry 1PK4) Resolution: 2.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 1.5 / Rfactor obs: 0.195 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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