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- PDB-8omk: hKHK-C in complex with ADP & fructose 1-phosphate -

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Basic information

Entry
Database: PDB / ID: 8omk
TitlehKHK-C in complex with ADP & fructose 1-phosphate
ComponentsKetohexokinase
KeywordsSUGAR BINDING PROTEIN / Ketohexokinase / KHK / product complex / sugar kinase
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
ADENOSINE-5'-DIPHOSPHATE / 1-O-phosphono-beta-D-fructofuranose / Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsEbenhoch, R. / Pautsch, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of BI-9787, a Potent Zwitterionic KHK-Inhibitor with Oral Bioavailability
Authors: Heine, N. / Weber, A. / Pautsch, A. / Gottschling, D. / Upheus, I. / Baur, M. / Ebenhoch, R. / Nosse, B. / Kley, J.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Jan 24, 2024Group: Data collection
Category: diffrn_detector / diffrn_radiation_wavelength ...diffrn_detector / diffrn_radiation_wavelength / diffrn_source / reflns / reflns_shell
Item: _diffrn_detector.type / _diffrn_radiation_wavelength.wavelength ..._diffrn_detector.type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_redundancy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4607
Polymers68,1532
Non-polymers1,3075
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-62 kcal/mol
Surface area24610 Å2
Unit cell
Length a, b, c (Å)82.809, 85.818, 137.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ketohexokinase / Hepatic fructokinase


Mass: 34076.586 Da / Num. of mol.: 2
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: Sugar ChemComp-F1X / 1-O-phosphono-beta-D-fructofuranose / beta D-Fructose 1-phosphate / 1-O-phosphono-beta-D-fructose / 1-O-phosphono-D-fructose / 1-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.477→85.8 Å / Num. obs: 34361 / % possible obs: 96.7 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.047 / Net I/σ(I): 15.2
Reflection shellResolution: 2.477→2.485 Å / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 309 / CC1/2: 0.873 / Rpim(I) all: 0.423 / % possible all: 87.3

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Processing

Software
NameClassification
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→39.64 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.307 / SU Rfree Blow DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1367 4 %RANDOM
Rwork0.2 ---
obs0.201 34201 96.7 %-
Displacement parametersBiso mean: 50.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.9016 Å20 Å20 Å2
2---5.7341 Å20 Å2
3---1.8325 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.48→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 80 265 4924
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089303HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0616786HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2045SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1539HARMONIC5
X-RAY DIFFRACTIONt_it9303HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion15.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion597SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9924SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.5 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2044 -2.77 %
Rwork0.2658 666 -
all0.2641 685 -
obs--93.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3451-0.441-0.20822.19831.07852.97720.05990.14440.2782-0.2733-0.08040.128-0.59220.01990.0205-0.0549-0.01260.0393-0.2401-0.0021-0.10680.10711.667115.9166
21.49650.1414-0.0731.15280.10571.35090.022-0.1613-0.2856-0.0209-0.0365-0.05110.11380.02060.0145-0.15050.03550.0287-0.06860.0542-0.0441-11.248419.293658.2102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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