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- PDB-8omd: Crystal structure of mKHK in complex with compound-4 -

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Basic information

Entry
Database: PDB / ID: 8omd
TitleCrystal structure of mKHK in complex with compound-4
ComponentsKetohexokinase
KeywordsSUGAR BINDING PROTEIN / Ketohexokinase / KHK / product complex / sugar kinase
Function / homologyKetohexokinase / ketohexokinase activity / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / fructose metabolic process / Ribokinase-like / compound / Ketohexokinase
Function and homology information
Biological speciesMus musculus (house mouse)
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,5478
Polymers138,6014
Non-polymers1,9474
Water5,098283
1
A: Ketohexokinase
C: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2744
Polymers69,3002
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-13 kcal/mol
Surface area24260 Å2
2
B: Ketohexokinase
D: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2744
Polymers69,3002
Non-polymers9732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-14 kcal/mol
Surface area24350 Å2
Unit cell
Length a, b, c (Å)47.420, 55.604, 136.632
Angle α, β, γ (deg.)91.40, 93.10, 115.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ketohexokinase


Mass: 34650.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Khk / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9YU79
#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.: 283 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 36 % MPD, 7.5 % PEG 8000, 0.1 M MES pH 5.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.92 Å / Num. obs: 80891 / % possible obs: 95.7 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.155 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.02 Å / Rmerge(I) obs: 0.721 / Num. unique obs: 1618 / CC1/2: 0.707

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Processing

Software
NameClassification
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.92 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.213 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4085 5.05 %RANDOM
Rwork0.235 ---
obs0.237 80891 95.7 %-
Displacement parametersBiso mean: 36.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.4091 Å2-0.8142 Å2-0.4633 Å2
2---3.3487 Å2-1.7724 Å2
3---5.7578 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9111 0 140 283 9534
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099435HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0712784HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3328SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1622HARMONIC5
X-RAY DIFFRACTIONt_it9435HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1171SEMIHARMONIC5
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_contact10696SEMIHARMONIC4
LS refinement shellResolution: 2→2.02 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1976 -4.64 %
Rwork0.1991 1543 -
all0.199 1618 -
obs--85.19 %
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)
10.66230.054-0.39710.4453-0.20642.32650.0443-0.03180.0968-0.0008-0.0339-0.023-0.07080.0866-0.0104-0.1301-0.0181-0.0179-0.15710.01970.0685-20.3578-29.7607-52.5906
20.5474-0.02440.28330.4552-0.12932.1730.05090.0365-0.0578-0.0052-0.0338-0.01340.04170.0784-0.0171-0.11480-0.0193-0.15810.01720.0649-44.0164-47.1584-86.0274
31.68290.2768-0.20041.0595-0.40731.4505-0.0301-0.1186-0.1179-0.00020.00820.01770.13970.00740.0219-0.1348-0.01-0.0051-0.19950.00880.042-38.4078-50.9424-19.6696
41.3658-0.15740.00260.8597-0.17911.1504-0.04180.10280.168-0.0373-0.0076-0.0315-0.1215-0.01580.0495-0.1242-0.0049-0.0245-0.19090.01670.0698-62.0568-26.0104-118.9464
50.0363-0.02150.0418-0.02080.0790.17080.02930.0399-0.01730.0183-0.0186-0.07-0.0120.1339-0.0107-0.1114-0.0287-0.0374-0.08260.07260.1916-30.6633-38.4499-69.2747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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