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Open data
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Basic information
Entry | Database: PDB / ID: 5ody | ||||||
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Title | Galectin-3C in complex with dithiogalactoside derivative | ||||||
![]() | Galectin-3![]() | ||||||
![]() | SUGAR BINDING PROTEIN / ![]() | ||||||
Function / homology | ![]() negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, R. / Peterson, K. / Nilsson, U.J. / Logan, D.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity. Authors: Peterson, K. / Kumar, R. / Stenstrom, O. / Verma, P. / Verma, P.R. / Hakansson, M. / Kahl-Knutsson, B. / Zetterberg, F. / Leffler, H. / Akke, M. / Logan, D.T. / Nilsson, U.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 82.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5oaxC ![]() 3zslS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 15701.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-9SK / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.19 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.1 M MgCl2, 0.4 M NaSCN, 7.9 mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.149→29.81 Å / Num. obs: 42774 / % possible obs: 98.73 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07061 / Rpim(I) all: 0.02917 / Net I/σ(I): 13.16 |
Reflection shell | Resolution: 1.149→1.19 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 3911 / CC1/2: 0.583 / Rpim(I) all: 0.4229 / % possible all: 91.85 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3ZSL Resolution: 1.149→29.81 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.149→29.81 Å
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Refine LS restraints |
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LS refinement shell |
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