+Open data
-Basic information
Entry | Database: PDB / ID: 1pml | ||||||
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Title | KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES | ||||||
Components | TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2 | ||||||
Keywords | HYDROLASE(SERINE PROTEASE) | ||||||
Function / homology | Function and homology information t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / serine protease inhibitor complex / plasminogen activation / platelet-derived growth factor receptor signaling pathway ...t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / serine protease inhibitor complex / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis / fibrinolysis / secretory granule / negative regulation of proteolysis / phosphoprotein binding / protein modification process / Schaffer collateral - CA1 synapse / blood coagulation / apical part of cell / response to hypoxia / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.38 Å | ||||||
Authors | Padmanabhan, K. / Tulinsky, A. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: Kringle-kringle interactions in multimer kringle structures. Authors: Padmanabhan, K. / Wu, T.P. / Ravichandran, K.G. / Tulinsky, A. #1: Journal: Biochemistry / Year: 1992 Title: Crystal Structure of the Kringle 2 Domain of Tissue Plasminogen Activator at 2.4 A Resolution Authors: De Vos, A.M. / Ultsch, M.H. / Kelly, R.F. / Padmanabhan, K. / Tulinsky, A. / Westbrook, M.L. / Kossiakoff, A.A. #2: Journal: Biochemistry / Year: 1991 Title: Crystal and Molecular Structure of Human Plasminogen Kringle 4 Refined to 1.9A Resolution Authors: Mulichak, A.M. / Tulinsky, A. / Ravichandran, K.G. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pml.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pml.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pml_validation.pdf.gz | 380.5 KB | Display | wwPDB validaton report |
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Full document | 1pml_full_validation.pdf.gz | 395.5 KB | Display | |
Data in XML | 1pml_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1pml_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/1pml ftp://data.pdbj.org/pub/pdb/validation_reports/pm/1pml | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99997, -0.0059, 0.024), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B. | |
-Components
#1: Protein | Mass: 9482.614 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00750, t-plasminogen activator #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.38 Å / Num. obs: 11621 / % possible obs: 91 % / Num. measured all: 30076 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.38 Å / Lowest resolution: 2.5 Å / % possible obs: 52 % / Num. possible: 2105 / Num. unique obs: 1101 / Mean I/σ(I) obs: 3.7 |
-Processing
Software | Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.38→8 Å / σ(F): 4 Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE INTERKRINGLE RESIDUES -3 - -2 IN MOLECULE A AND MOLECULE B AND -3 - -2 AND 82 IN MOLECULE C.
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Refinement step | Cycle: LAST / Resolution: 2.38→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.145 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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