+Open data
-Basic information
Entry | Database: PDB / ID: 1ddj | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN | ||||||
Components | PLASMINOGENPlasmin | ||||||
Keywords | BLOOD CLOTTING / PLASMINOGEN / CATALYTIC DOMAIN | ||||||
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 / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Wang, X. / Terzyan, S. / Tang, J. / Loy, J. / Lin, X. / Zhang, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Human plasminogen catalytic domain undergoes an unusual conformational change upon activation. Authors: Wang, X. / Terzyan, S. / Tang, J. / Loy, J.A. / Lin, X. / Zhang, X.C. #1: Journal: Science / Year: 1998 Title: Crystal structure of the catalytic domain of human plasmin complexed with streptokinase Authors: Wang, X. / Lin, X. / Loy, J.A. / Tang, J. / Zhang, X.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddj.cif.gz | 206.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddj.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ddj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddj ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27080.135 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN / Mutation: S741A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / References: UniProt: P00747, plasmin #2: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.57 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, SODIUM CHLORIDE, ISOPROPANOL, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting dropDetails: drop solution was mixed 1:1 with the reservoir solution | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.04 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Mar 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2→23 Å / Num. all: 58496 / Num. obs: 58496 / % possible obs: 82.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.4 / % possible all: 78.4 |
Reflection shell | *PLUS % possible obs: 78.4 % / Num. unique obs: 5533 |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: A BULK SOLVENT CORRECTION AND AN ANISOTROPIC OVERALL B FACTOR REFINEMENT WERE APPLIED
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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