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Yorodumi- PDB-6w4z: Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w4z | ||||||
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Title | Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside | ||||||
Components | Galectin-8 | ||||||
Keywords | SUGAR BINDING PROTEIN / Galectin-8N | ||||||
Function / homology | Function and homology information lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Patel, B. / Kishor, C. / Blanchard, H. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Rational Design and Synthesis of Methyl-beta-d-galactomalonyl Phenyl Esters as Potent Galectin-8 N Antagonists. Authors: Patel, B. / Kishor, C. / Houston, T.A. / Shatz-Azoulay, H. / Zick, Y. / Vinik, Y. / Blanchard, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w4z.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w4z.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 6w4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w4z_validation.pdf.gz | 976.9 KB | Display | wwPDB validaton report |
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Full document | 6w4z_full_validation.pdf.gz | 983 KB | Display | |
Data in XML | 6w4z_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6w4z_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/6w4z ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w4z | HTTPS FTP |
-Related structure data
Related structure data | 5t7sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17291.928 Da / Num. of mol.: 2 / Mutation: M54V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214 |
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-Non-polymers , 5 types, 144 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate dihydrate pH 5.6, 20% PEG 4000, 10% IPA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→46.32 Å / Num. obs: 41190 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.538 / Num. unique obs: 1987 / CC1/2: 0.805 / Rpim(I) all: 0.946 / Χ2: 0.84 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T7S Resolution: 1.59→46.31 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.883 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.096 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: 19.814 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→46.31 Å
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Refine LS restraints |
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LS refinement shell |
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