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Yorodumi- PDB-2pk4: THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF... -
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-Basic information
Entry | Database: PDB / ID: 2pk4 | |||||||||
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Title | THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF HUMAN PLASMINOGEN KRINGLE | |||||||||
Components | HUMAN PLASMINOGEN KRINGLE 4 | |||||||||
Keywords | HYDROLASE(SERINE PROTEASE) | |||||||||
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 | X-RAY DIFFRACTION / Resolution: 2.25 Å | |||||||||
Authors | Tulinsky, A. / Wu, T.-P. | |||||||||
Citation | Journal: Biochemistry / Year: 1991 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. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H. #2: Journal: Blood Coagulation Fibrinolysis / Year: 1990 Title: Structure of the Lysine-Fibrin Binding Subsite of Human Plasminogen Kringle 4 Authors: Mulichak, A.M. / Tulinsky, A. #3: Journal: Proteins / Year: 1988 Title: Lysine(Slash)Fibrin Binding Sites of Kringles Modeled After the Structure of Kringle 1 of Prothrombin Authors: Tulinsky, A. / Park, C.H. / Mao, B. / Llinas, M. #4: Journal: J.Mol.Biol. / Year: 1988 Title: Structure of Prothrombin Fragment 1 Refined at 2.8 Angstroms Resolution Authors: Tulinsky, A. / Park, C.H. / Skrzypczak-Jankun, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pk4.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pk4.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pk4 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pk4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 30 |
-Components
#1: Protein | Mass: 9169.110 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00747 |
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#2: Chemical | ChemComp-ACA / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE NUMBERING OF KRINGLE 4 IS BASED ON PLASMINOGEN KRINGLE 5. THE FINAL STRUCTURE HAS RESIDUE ...SEQUENCE NUMBERING OF KRINGLE 4 IS BASED ON PLASMINOGE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.16 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.25 Å / Num. all: 3400 / Num. obs: 3381 / % possible obs: 95 % |
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-Processing
Software | Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.148 / Highest resolution: 2.25 Å Details: RESIDUES THR 18 AND ARG 32 HAD NO ELECTRON DENSITY AND WERE THEREFORE REFINED AS ALA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.25 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 7 Å / Num. reflection obs: 2993 / Rfactor obs: 0.148 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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