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- PDB-5e89: Crystal structure of Human galectin-3 CRD in complex with 3-fluop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5.0E+89 | ||||||
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Title | Crystal structure of Human galectin-3 CRD in complex with 3-fluophenyl-1,2,3-triazolyl thiodigalactoside inhibitor | ||||||
![]() | Galectin-3![]() | ||||||
![]() | SUGAR BINDING PROTEIN/INHIBITOR / 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: Galectin-3-Binding Glycomimetics that Strongly Reduce Bleomycin-Induced Lung Fibrosis and Modulate Intracellular Glycan Recognition. Authors: Delaine, T. / Collins, P. / MacKinnon, A. / Sharma, G. / Stegmayr, J. / Rajput, V.K. / Mandal, S. / Cumpstey, I. / Larumbe, A. / Salameh, B.A. / Kahl-Knutsson, B. / van Hattum, H. / van ...Authors: Delaine, T. / Collins, P. / MacKinnon, A. / Sharma, G. / Stegmayr, J. / Rajput, V.K. / Mandal, S. / Cumpstey, I. / Larumbe, A. / Salameh, B.A. / Kahl-Knutsson, B. / van Hattum, H. / van Scherpenzeel, M. / Pieters, R.J. / Sethi, T. / Schambye, H. / Oredsson, S. / Leffler, H. / Blanchard, H. / 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 | ![]() | 81.3 KB | Display | ![]() |
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PDB format | ![]() | 58.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5e88C ![]() 5e8aC ![]() 2nn8S 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: 15758.100 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 114-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / ![]() |
#3: Chemical | ChemComp-TD2 / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.22 % |
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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: May 11, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.497→43.015 Å / Num. all: 21173 / Num. obs: 21173 / % possible obs: 92.4 % / Redundancy: 5.5 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Rsym value: 0.046 / Net I/av σ(I): 9.806 / Net I/σ(I): 18.2 / Num. measured all: 115525 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5→43.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1941 / WRfactor Rwork: 0.1745 / FOM work R set: 0.8788 / SU B: 2.736 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0829 / SU Rfree: 0.0791 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.079 / 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: 60.45 Å2 / Biso mean: 16.488 Å2 / Biso min: 6.11 Å2
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Refinement step | Cycle: final / Resolution: 1.5→43.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.497→1.536 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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