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- PDB-5eqg: Human GLUT1 in complex with inhibitor (2~{S})-3-(4-fluorophenyl)-... -

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Basic information

Entry
Database: PDB / ID: 5eqg
TitleHuman GLUT1 in complex with inhibitor (2~{S})-3-(4-fluorophenyl)-2-[2-(3-hydroxyphenyl)ethanoylamino]-~{N}-[(1~{S})-1-phenylethyl]propanamide
ComponentsSolute carrier family 2, facilitated glucose transporter member 1
KeywordsTRANSPORT 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 / fucose transmembrane transporter activity / response to Thyroglobulin triiodothyronine / dehydroascorbic acid transmembrane transporter activity / Lactose synthesis / dehydroascorbic acid transport / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process ...glucose transporter complex / Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) / long-chain fatty acid import across plasma membrane / fucose transmembrane transporter activity / response to Thyroglobulin triiodothyronine / dehydroascorbic acid transmembrane transporter activity / Lactose synthesis / dehydroascorbic acid transport / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / D-glucose import across plasma membrane / Cellular hexose transport / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / photoreceptor cell maintenance / female germ cell nucleus / cellular hyperosmotic response / female pronucleus / long-chain fatty acid transmembrane transporter activity / cortical actin cytoskeleton / D-glucose import / intercalated disc / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / cellular response to glucose starvation / photoreceptor inner segment / central nervous system development / Regulation of insulin secretion / cellular response to mechanical stimulus / female pregnancy / response to insulin / sarcolemma / cerebral cortex development / caveola / kinase binding / Z disc / melanosome / presynapse / protein-containing complex assembly / midbody / blood microparticle / basolateral plasma membrane / response to hypoxia / apical plasma membrane / Golgi membrane / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Glucose transporter, type 1 (GLUT1) / Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; ...Glucose transporter, type 1 (GLUT1) / Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5RE / Solute carrier family 2, facilitated glucose transporter member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKapoor, 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
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485 United States
Danish Council for Independent ResearchDFF-4002-00052 Denmark
European Research Council (ERC)637372European Union
CitationJournal: 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
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.5Feb 5, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 2, facilitated glucose transporter member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5462
Polymers54,1251
Non-polymers4201
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.338, 102.497, 68.162
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Solute carrier family 2, facilitated glucose transporter member 1 / Glucose transporter type 1 / erythrocyte/brain / GLUT-1 / HepG2 glucose transporter


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
#2: Chemical ChemComp-5RE / (2~{S})-3-(4-fluorophenyl)-2-[2-(3-hydroxyphenyl)ethanoylamino]-~{N}-[(1~{S})-1-phenylethyl]propanamide


Mass: 420.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25FN2O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.8→3 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PYP

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
RfactorNum. reflection% reflection
Rfree0.2807 937 5.11 %
Rwork0.2352 --
obs0.2375 18319 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→67.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 31 0 3495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033580
X-RAY DIFFRACTIONf_angle_d0.5844862
X-RAY DIFFRACTIONf_dihedral_angle_d13.2342072
X-RAY DIFFRACTIONf_chiral_restr0.039567
X-RAY DIFFRACTIONf_plane_restr0.004603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.0530.4131370.38912481X-RAY DIFFRACTION100
3.053-3.24430.35871430.33552449X-RAY DIFFRACTION100
3.2443-3.49470.33571380.27882463X-RAY DIFFRACTION100
3.4947-3.84640.27681310.23592480X-RAY DIFFRACTION100
3.8464-4.40290.24691390.19922485X-RAY DIFFRACTION100
4.4029-5.54680.22871340.20332485X-RAY DIFFRACTION100
5.5468-67.23460.28681150.22422539X-RAY DIFFRACTION99

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