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Open data
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Basic information
Entry | Database: PDB / ID: 1snt | ||||||
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Title | Structure of the human cytosolic sialidase Neu2 | ||||||
![]() | Sialidase 2 | ||||||
![]() | HYDROLASE / sialidase / neuraminidase / ganglioside | ||||||
Function / homology | ![]() Sialic acid metabolism / glycoprotein catabolic process / glycosphingolipid catabolic process / exo-alpha-sialidase activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity ...Sialic acid metabolism / glycoprotein catabolic process / glycosphingolipid catabolic process / exo-alpha-sialidase activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / catalytic complex / lysosome / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chavas, L.M.G. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Kato, R. / Monti, E. / Wakatsuki, S. | ||||||
![]() | ![]() Title: Crystal Structure of the Human Cytosolic Sialidase Neu2: EVIDENCE FOR THE DYNAMIC NATURE OF SUBSTRATE RECOGNITION Authors: Chavas, L.M.G. / Tringali, C. / Fusi, P. / Venerando, B. / Tettamanti, G. / Kato, R. / Monti, E. / Wakatsuki, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.1 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1so7C ![]() 1vcuC ![]() 1eusS 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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Unit cell |
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Components
#1: Protein | Mass: 42419.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: sodium potassium phosphate, sodium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 51301 / Num. obs: 51297 / % possible obs: 99.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.75→1.84 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EUS Resolution: 1.75→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: About CD1/CD2 (LEU A 90) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, the author assigned as ...Details: About CD1/CD2 (LEU A 90) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, the author assigned as a double conformation only one of the atoms.(CD2 of LEU 90 and CG1 of VAL 325) Thus the occupancies of the alternate conformations are greater than 1.00 and there are chirality errors at these atoms.
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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