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- PDB-4zw9: Crystal structure of human GLUT3 bound to D-glucose in the outwar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zw9 | ||||||
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Title | Crystal structure of human GLUT3 bound to D-glucose in the outward-occluded conformation at 1.5 angstrom | ||||||
![]() | Solute carrier family 2, facilitated glucose transporter member 3 | ||||||
![]() | TRANSPORT PROTEIN / transporter | ||||||
Function / homology | ![]() galactose transmembrane transporter activity / galactose transmembrane transport / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / D-glucose transmembrane transporter activity / Cellular hexose transport / glucose transmembrane transporter activity / glucose import across plasma membrane / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process ...galactose transmembrane transporter activity / galactose transmembrane transport / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / D-glucose transmembrane transporter activity / Cellular hexose transport / glucose transmembrane transporter activity / glucose import across plasma membrane / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / glucose transmembrane transport / D-glucose binding / aggresome / glucose import / tertiary granule membrane / ficolin-1-rich granule membrane / transport across blood-brain barrier / specific granule membrane / MECP2 regulates neuronal receptors and channels / secretory granule membrane / cell projection / perikaryon / carbohydrate metabolic process / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, D. / Sun, P.C. / Yan, C.Y. / Yan, N. | ||||||
![]() | ![]() Title: Molecular basis of ligand recognition and transport by glucose transporters Authors: Deng, D. / Sun, P.C. / Yan, C.Y. / Ke, M. / Jiang, X. / Xiong, L. / Ren, W. / Hirata, K. / Yamamoto, M. / Fan, S. / Yan, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.7 KB | Display | ![]() |
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PDB format | ![]() | 157.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1017.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zwbC ![]() 4zwcC ![]() 4pypS 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: 56474.492 Da / Num. of mol.: 1 / Mutation: N43T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Sugar | ChemComp-GLC / | #4: Sugar | ChemComp-BGC / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.8 Details: 28%(v/v) PEG400, 0.1M HEPES, 50 mM ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 88120 / % possible obs: 98.8 % / Redundancy: 18 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.6 / % possible all: 91.8 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4pyp Resolution: 1.502→30.226 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.15 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.502→30.226 Å
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Refine LS restraints |
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LS refinement shell |
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