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Yorodumi- PDB-5eqg: Human GLUT1 in complex with inhibitor (2~{S})-3-(4-fluorophenyl)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eqg | ||||||||||||
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Title | Human GLUT1 in complex with inhibitor (2~{S})-3-(4-fluorophenyl)-2-[2-(3-hydroxyphenyl)ethanoylamino]-~{N}-[(1~{S})-1-phenylethyl]propanamide | ||||||||||||
Components | Solute carrier family 2, facilitated glucose transporter member 1 | ||||||||||||
Keywords | TRANSPORT PROTEIN/INHIBITOR / MFS transporter / glucose transporter / TRANSPORT PROTEIN-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information glucose transporter complex / Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) / long-chain fatty acid import across plasma membrane / response to Thyroglobulin triiodothyronine / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / Lactose synthesis / glucose transmembrane transporter activity / D-glucose transmembrane transporter activity / Vitamin C (ascorbate) metabolism ...glucose transporter complex / Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) / long-chain fatty acid import across plasma membrane / response to Thyroglobulin triiodothyronine / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / Lactose synthesis / glucose transmembrane transporter activity / D-glucose transmembrane transporter activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Cellular hexose transport / glucose import across plasma membrane / glucose transmembrane transport / cellular hyperosmotic response / photoreceptor cell maintenance / female germ cell nucleus / female pronucleus / long-chain fatty acid transmembrane transporter activity / cortical actin cytoskeleton / glucose import / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / intercalated disc / cellular response to glucose starvation / photoreceptor inner segment / central nervous system development / Regulation of insulin secretion / female pregnancy / caveola / sarcolemma / response to insulin / cerebral cortex development / Z disc / kinase binding / cellular response to mechanical stimulus / : / melanosome / presynapse / midbody / basolateral plasma membrane / protein-containing complex assembly / blood microparticle / response to hypoxia / apical plasma membrane / Golgi membrane / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Kapoor, K. / Finer-Moore, J. / Pedersen, B.P. / Caboni, L. / Waight, A.B. / Hillig, R. / Bringmann, P. / Heisler, I. / Muller, T. / Siebeneicher, H. / Stroud, R.M. | ||||||||||||
Funding support | United States, Denmark, European Union, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Mechanism of inhibition of human glucose transporter GLUT1 is conserved between cytochalasin B and phenylalanine amides. Authors: Kapoor, K. / Finer-Moore, J.S. / Pedersen, B.P. / Caboni, L. / Waight, A. / Hillig, R.C. / Bringmann, P. / Heisler, I. / Muller, T. / Siebeneicher, H. / Stroud, R.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eqg.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eqg.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 5eqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/5eqg ftp://data.pdbj.org/pub/pdb/validation_reports/eq/5eqg | HTTPS FTP |
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-Related structure data
Related structure data | 5eqhC 5eqiC 4pypS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54125.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A1, GLUT1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DSY-5 / References: UniProt: P11166 |
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#2: Chemical | ChemComp-5RE / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.15 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 30-40% v/v PEG400, 100 mM MES, pH 5.5-6.5, 50-200 mM sodium chloride or magnesium chloride PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→77.84 Å / Num. all: 20352 / Num. obs: 20352 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PYP Resolution: 2.9→67.217 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.96 / 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: 2.9→67.217 Å
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Refine LS restraints |
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LS refinement shell |
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