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- PDB-8ome: Crystal structure of hKHK-A in complex with compound-4 -

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Basic information

Entry
Database: PDB / ID: 8ome
TitleCrystal structure of hKHK-A in complex with compound-4
ComponentsKetohexokinase
KeywordsSUGAR BINDING PROTEIN / Ketohexokinase / KHK / inhibitor bound / sugar kinase / isoform selectivity
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Ketohexokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
compound / Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEbenhoch, R. / Pautsch, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design.
Authors: Ebenhoch, R. / Bauer, M. / Romig, H. / Gottschling, D. / Kley, J.T. / Heine, N. / Weber, A. / Uphues, I. / Nar, H. / Pautsch, A.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
C: Ketohexokinase
D: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0208
Polymers131,0734
Non-polymers1,9474
Water9,458525
1
A: Ketohexokinase
D: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5104
Polymers65,5372
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-9 kcal/mol
Surface area24450 Å2
2
B: Ketohexokinase
C: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5104
Polymers65,5372
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-9 kcal/mol
Surface area24080 Å2
Unit cell
Length a, b, c (Å)66.151, 73.564, 82.685
Angle α, β, γ (deg.)82.24, 72.81, 74.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ketohexokinase / Hepatic fructokinase


Mass: 32768.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Production host: Escherichia coli (E. coli) / References: UniProt: P50053, ketohexokinase
#2: Chemical
ChemComp-VTJ / compound


Mass: 486.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H30N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 15 % PEG 3350, 0.1 M ammonium formate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→61.3 Å / Num. obs: 81531 / % possible obs: 87.9 % / Redundancy: 1.9 % / CC1/2: 1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.028→2.035 Å / Num. unique obs: 81531 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→61.3 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.231 --RANDOM
Rwork0.201 ---
obs-81531 87.9 %-
Refinement stepCycle: LAST / Resolution: 2→61.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9141 0 140 525 9806

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