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- PDB-5wzo: Crystal structure of human secreted phospholipase A2 group IIE, c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wzo | ||||||
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Title | Crystal structure of human secreted phospholipase A2 group IIE, crystallized with calcium | ||||||
![]() | Group IIE secretory phospholipase A2 | ||||||
![]() | HYDROLASE/INHIBITOR / inhibitor / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / low-density lipoprotein particle remodeling ...Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / low-density lipoprotein particle remodeling / calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / inflammatory response / calcium ion binding / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hou, S. / Xu, J. / Xu, T. / Liu, J. | ||||||
![]() | ![]() Title: Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2 group IIE Authors: Hou, S. / Xu, T. / Xu, J. / Qu, L. / Xu, Y. / Chen, L. / Liu, 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 | ![]() | 42.1 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976.3 KB | Display | ![]() |
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Full document | ![]() | 979.3 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wzmC ![]() 5wzsC ![]() 5wztC ![]() 5wzuC ![]() 5wzvC ![]() 5wzwC ![]() 5y5eC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13986.137 Da / Num. of mol.: 1 / Fragment: UNP residues 20-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 208 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-B3P / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Aug 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.76 Å / Num. obs: 15248 / % possible obs: 98.5 % / Redundancy: 8.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.778 / CC1/2: 0.64 / Rpim(I) all: 0.402 / Rrim(I) all: 0.883 / % possible all: 85.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.9 Å2 / Biso mean: 18.662 Å2 / Biso min: 6.04 Å2
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Refinement step | Cycle: final / Resolution: 1.9→18.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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