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Yorodumi- PDB-2f27: Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f27 | ||||||
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Title | Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double Mutant in Complex with DANA Inhibitor | ||||||
Components | Sialidase 2 | ||||||
Keywords | HYDROLASE / SIALIDASE / NEURAMINIDASE / GANGLIOSIDE / DRUG DESIGN | ||||||
Function / homology | Function and homology information 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Chavas, L.M.G. / Kato, R. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Monti, E. / Wakatsuki, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Human Sialidase Neu2 E111Q-Q112E Double Mutant in Complex with DANA Inhibitor Authors: Chavas, L.M.G. / Kato, R. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Monti, E. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f27.cif.gz | 162.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f27.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f27_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2f27_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2f27_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 2f27_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/2f27 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/2f27 | HTTPS FTP |
-Related structure data
Related structure data | 1sntS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a monomer. There are 2 biological units in the asymmetric unit (chain A and chain B) |
-Components
#1: Protein | Mass: 42419.598 Da / Num. of mol.: 2 / Mutation: E111Q Q112E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y3R4, exo-alpha-sialidase #2: Sugar | #3: Chemical | ChemComp-EPE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2-deoxy-2,3-dehydro-N-acetyl neuraminic acid, 2-methyl-2,4-pentanediol, guanidine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→79.06 Å / Num. all: 48894 / Num. obs: 48518 / % possible obs: 99.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SNT Resolution: 2.15→79.06 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 50.622 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.866 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→79.06 Å
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Refine LS restraints |
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Xplor file |
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