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- PDB-6ul7: Structure of human ketohexokinase-C in complex with fructose, NO3... -

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Basic information

Entry
Database: PDB / ID: 6ul7
TitleStructure of human ketohexokinase-C in complex with fructose, NO3, and osthole
ComponentsKetohexokinase
KeywordsTRANSFERASE / beta-clasp / sugar kinase / PfKB family / KHK / ketohexokinase / fructose / osthole
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion ...Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ketohexokinase / : / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one / beta-D-fructofuranose / NITRATE ION / Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGasper, W.C. / Gardner, S. / Allen, K.N. / Tolan, D.R.
CitationJournal: To be Published
Title: Structure of human ketohexokinase-C in complex with fructose, NO3, and osthole
Authors: Gasper, W.C. / Gardner, S. / Ross, A. / Allen, K.N. / Tolan, D.R.
History
DepositionOct 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2204
Polymers34,7331
Non-polymers4863
Water3,585199
1
A: Ketohexokinase
hetero molecules

A: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4408
Polymers69,4672
Non-polymers9736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4380 Å2
ΔGint3 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.870, 106.870, 79.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

21A-478-

HOH

31A-591-

HOH

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Components

#1: Protein Ketohexokinase / Hepatic fructokinase / Ketohexokinase-C


Mass: 34733.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50053, ketohexokinase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-A0O / 7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one


Mass: 244.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H16O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate, 1.3 M potassium nitrate, 100 mM magnesium chloride, 220 mM fructose, 3.8 mM osthole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→47.79 Å / Num. obs: 20332 / % possible obs: 97 % / Redundancy: 46.4 % / Biso Wilson estimate: 33.25 Å2 / CC1/2: 0.97 / Net I/σ(I): 18.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1568 / CC1/2: 0.83 / % possible all: 76

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Processing

Software
NameVersionClassification
SADABSdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
SAINTdata reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3Q92

3q92


Resolution: 2.3→47.79 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2779 1765 -
Rwork0.2291 --
obs-20007 95.74 %
Displacement parametersBiso max: 78.55 Å2 / Biso mean: 33.252 Å2 / Biso min: 12.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 34 199 2509
LS refinement shellResolution: 2.3001→2.3823 Å
RfactorNum. reflection
Rfree0.3456 -
Rwork0.3419 -
obs-1834

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