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- PDB-7vu9: Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vu9 | ||||||
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Title | Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)[GlcNAc(beta1-4)]GlcNAc | ||||||
![]() | Lectin (PhoSL) | ||||||
![]() | SUGAR BINDING PROTEIN / Lectin / Trimer / Fucose | ||||||
Function / homology | FORMIC ACID / Lectin (PhoSL)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamasaki, K. / Yamasaki, T. / Kubota, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Core fucose-specific Pholiota squarrosa lectin (PhoSL) as a potent broad-spectrum inhibitor of SARS-CoV-2 infection. Authors: Yamasaki, K. / Adachi, N. / Ngwe Tun, M.M. / Ikeda, A. / Moriya, T. / Kawasaki, M. / Yamasaki, T. / Kubota, T. / Nagashima, I. / Shimizu, H. / Tateno, H. / Morita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a86S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 4440.958 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4.3 M sodium formate (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.154→44.87 Å / Num. obs: 17730 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.18 |
Reflection shell | Resolution: 2.154→2.28 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 5358 / CC1/2: 0.684 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A86 Resolution: 2.154→44.865 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.909 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.199 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.896 Å2
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Refinement step | Cycle: LAST / Resolution: 2.154→44.865 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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