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Open data
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Basic information
Entry | Database: PDB / ID: 4y1v | |||||||||||||||
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Title | Complex of human Galectin-1 and Galbeta1-3GlcNAc | |||||||||||||||
![]() | Galectin-1 | |||||||||||||||
![]() | SUGAR BINDING PROTEIN / Complex / Galectin-1 / lectin / type 1 LacNAc | |||||||||||||||
Function / homology | ![]() galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | Lin, H.Y. / Hsieh, T.J. / Lin, C.H. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of human galectin-1 inhibition with Ki values in the micro- to nanomolar range Authors: Lin, H.Y. / Hsieh, T.J. / Tu, Z. / Huang, B.S. / Wu, S.C. / Chien, C.T. / Hsu, S.T. / Lin, C.H. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.8 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y1uC ![]() 4y1xC ![]() 4y1yC ![]() 4y1zC ![]() 4y20C ![]() 4y22C ![]() 4y26C ![]() 1w6nS 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: 16910.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N-terminus residues are missing due to disorder. Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris (pH 8.0), 0.2 M Li2SO4, 30% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→30 Å / Num. obs: 12886 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.79 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.022 / Rrim(I) all: 0.047 / Χ2: 0.907 / Net I/av σ(I): 30.454 / Net I/σ(I): 18.2 / Num. measured all: 57534 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1W6N Resolution: 2.32→25.833 Å / FOM work R set: 0.8109 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 24.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.15 Å2 / Biso mean: 38.4 Å2 / Biso min: 16.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→25.833 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: 9
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Refinement TLS params. | Method: refined / Origin x: 11.3375 Å / Origin y: -22.3516 Å / Origin z: -12.6699 Å
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Refinement TLS group | Selection details: all |