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- PDB-5exo: Crystal structure of Human galectin-3 CRD in complex with methyl ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5exo | ||||||
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Title | Crystal structure of Human galectin-3 CRD in complex with methyl 2-O-acetyl-3-O-(2H-chromene-3-yl-methyl)-a-D-galactopyranoside inhibitor | ||||||
![]() | Galectin-3![]() | ||||||
![]() | SUGAR BINDING PROTEIN / CARBOHYDRATE-RECOGNITION / ![]() ![]() | ||||||
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 | ![]() ![]() | ||||||
![]() | Collins, P.M. / Blanchard, H. | ||||||
![]() | ![]() Title: A Selective Galactose-Coumarin-Derived Galectin-3 Inhibitor Demonstrates Involvement of Galectin-3-glycan Interactions in a Pulmonary Fibrosis Model. Authors: Rajput, V.K. / MacKinnon, A. / Mandal, S. / Collins, P. / Blanchard, H. / Leffler, H. / Sethi, T. / Schambye, H. / Mukhopadhyay, B. / 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 | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2nn8S 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: 15758.100 Da / Num. of mol.: 1 / Fragment: RESIDUES 112-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / ![]() |
#3: Chemical | ChemComp-5SY / [( |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 31% PEG 6000, 100MM MGCL2, 8MM BETA MERCEPTOETHANOL, 100MM TRIS HCL |
-Data collection
Diffraction | Mean temperature: 293 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jan 31, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.502→43.122 Å / Num. all: 21563 / Num. obs: 21563 / % possible obs: 95 % / Redundancy: 5.2 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.057 / Rsym value: 0.053 / Net I/av σ(I): 7.363 / Net I/σ(I): 16.3 / Num. measured all: 113115 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2nn8 Resolution: 1.502→43.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1977 / WRfactor Rwork: 0.1674 / FOM work R set: 0.8665 / SU B: 2.647 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0729 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.97 Å2 / Biso mean: 17.641 Å2 / Biso min: 6.74 Å2
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Refinement step | Cycle: final / Resolution: 1.502→43.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.1784 Å / Origin y: 0.8207 Å / Origin z: 6.5304 Å
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