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Open data
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Basic information
Entry | Database: PDB / ID: 5fic | |||||||||
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Title | Open form of murine Acid Sphingomyelinase in presence of lipid | |||||||||
![]() | Sphingomyelin phosphodiesterase | |||||||||
![]() | HYDROLASE / SMPD1 / ASM / ASMase / saposin | |||||||||
Function / homology | ![]() acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / Glycosphingolipid catabolism / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / ceramide metabolic process ...acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / Glycosphingolipid catabolism / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / ceramide metabolic process / ceramide biosynthetic process / plasma membrane repair / hydrolase activity, acting on glycosyl bonds / response to type I interferon / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / positive regulation of protein dephosphorylation / cellular response to calcium ion / cholesterol metabolic process / response to interleukin-1 / lipid droplet / response to cocaine / wound healing / response to virus / cellular response to UV / positive regulation of viral entry into host cell / lysosome / response to xenobiotic stimulus / symbiont entry into host cell / positive regulation of apoptotic process / extracellular space / zinc ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gorelik, A. / Illes, K. / Heinz, L.X. / Superti-Furga, G. / Nagar, B. | |||||||||
![]() | ![]() Title: Crystal structure of mammalian acid sphingomyelinase. Authors: Gorelik, A. / Illes, K. / Heinz, L.X. / Superti-Furga, G. / Nagar, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 777.7 KB | Display | ![]() |
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PDB format | ![]() | 656.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 71.6 KB | Display | |
Data in CIF | ![]() | 96.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fi9C ![]() 5fibC ![]() 5hqnC ![]() 5hnqS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 60431.633 Da / Num. of mol.: 4 / Fragment: UNP residues 84-611 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04519, sphingomyelin phosphodiesterase |
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-Sugars , 4 types, 8 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | |
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-Non-polymers , 5 types, 61 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/6E0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/6E0.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-CL / #8: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium/potassium phosphate, MES, sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97959 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.318 Å / Num. obs: 99971 / % possible obs: 100 % / Redundancy: 6.725 % / Net I/σ(I): 9.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HNQ Resolution: 2.8→49.318 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 23.76 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.318 Å
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Refine LS restraints |
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LS refinement shell |
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