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- PDB-2azy: Crystal Structure of Porcine Pancreatic Phospholipase A2 in Compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2azy | ||||||
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Title | Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Cholate | ||||||
![]() | Phospholipase A2, major isoenzyme | ||||||
![]() | HYDROLASE / Bile salt / cholate / CARBOXYLIC ESTER HYDROLASE / PLA2 / Pancreatic Enzyme | ||||||
Function / homology | ![]() positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding ...positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of MAP kinase activity / phospholipid binding / fatty acid biosynthetic process / cellular response to insulin stimulus / positive regulation of immune response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pan, Y.H. / Bahnson, B.J. / Jain, M.K. | ||||||
![]() | ![]() Title: Structural basis for bile salt inhibition of pancreatic phospholipase A2. Authors: Pan, Y.H. / Bahnson, B.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 | ![]() | 44.2 KB | Display | ![]() |
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PDB format | ![]() | 29.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 745.9 KB | Display | ![]() |
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Full document | ![]() | 749.8 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2azzC ![]() 2b00C ![]() 2b01C ![]() 2b03C ![]() 2b04C ![]() 2bo1S C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14009.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CHD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 8%PEG8K, pH 8.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2004 / Details: mirrors |
Radiation | Monochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35 Å / Num. obs: 14784 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.038 / Χ2: 1.5 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible obs: 93.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6 / Num. measured obs: 1333 / Rsym value: 0.255 / Χ2: 1.25 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2BO1 Resolution: 1.9→35 Å / Cross valid method: THROUGHT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→35 Å
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Refine LS restraints |
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Xplor file |
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