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Open data
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Basic information
Entry | Database: PDB / ID: 6l6a | ||||||
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Title | X-ray structure of human galectin-10 in complex with D-mannose | ||||||
![]() | Galectin-10 | ||||||
![]() | SUGAR BINDING PROTEIN / beta-sandwich structure / lectin | ||||||
Function / homology | ![]() regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate binding / collagen-containing extracellular matrix / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kamitori, S. | ||||||
![]() | ![]() Title: Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals. Authors: Itoh, A. / Nonaka, Y. / Nakakita, S.I. / Yoshida, H. / Nishi, N. / Nakamura, T. / Kamitori, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.4 KB | Display | ![]() |
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PDB format | ![]() | 30.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6l64C ![]() 6l67C ![]() 6l68C ![]() 6l6bC ![]() 6l6cC ![]() 6l6dC ![]() 1qkqS S: Starting model for refinement 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 on special symmetry positions |
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Components
#1: Protein | Mass: 16644.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-BMA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→19.34 Å / Num. obs: 17615 / % possible obs: 98 % / Redundancy: 19.2 % / CC1/2: 0.997 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.81→1.86 Å / Num. unique obs: 1196 / CC1/2: 0.918 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QKQ Resolution: 1.81→19.338 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.19 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.113 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.726 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→19.338 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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