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- PDB-6qje: Structure of human galactokinase 1 bound with 4-{[2-(Methylsulfon... -

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Basic information

Entry
Database: PDB / ID: 6qje
TitleStructure of human galactokinase 1 bound with 4-{[2-(Methylsulfonyl)-1H-imidazol-1-yl]methyl}-1,3-thiazole
ComponentsGalactokinase
KeywordsTRANSFERASE / GALK1 / fragment / fragment-bound / galactokinase 1 / sugar kinase
Function / homology
Function and homology information


glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose catabolic process via UDP-galactose / galactose binding / galactose metabolic process ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose catabolic process via UDP-galactose / galactose binding / galactose metabolic process / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Chem-HFK / Chem-J4Q / Galactokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. ...Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / Lai, K. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of human galactokinase 1 bound with 4-{[2-(Methylsulfonyl)-1H-imidazol-1-yl]methyl}-1,3-thiazole
Authors: Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / Lai, K. / Yue, W.W.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,25814
Polymers168,8404
Non-polymers2,41810
Water3,099172
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9844
Polymers42,2101
Non-polymers7743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9844
Polymers42,2101
Non-polymers7743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8374
Polymers42,2101
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4532
Polymers42,2101
Non-polymers2431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.703, 114.873, 121.044
Angle α, β, γ (deg.)90.000, 100.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 7 molecules ABCD

#1: Protein
Galactokinase / / Galactose kinase


Mass: 42209.973 Da / Num. of mol.: 4 / Mutation: K252A, E253A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51570, galactokinase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 179 molecules

#3: Chemical ChemComp-HFK / 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one


Mass: 350.414 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H22N4O2
#4: Chemical ChemComp-J4Q / 4-[(2-methylsulfonylimidazol-1-yl)methyl]-1,3-thiazole


Mass: 243.306 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H9N3O2S2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ...Details: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.4→82.65 Å / Num. obs: 126441 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.059 / Rrim(I) all: 0.11 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.04-2.153.41.9184160.4741.2062.25699.8
6.44-82.653.30.02640820.9990.0170.03199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wuu

1wuu


Resolution: 2.4→82.646 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.61
RfactorNum. reflection% reflection
Rfree0.269 3918 5.08 %
Rwork0.217 --
obs0.2196 77082 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.58 Å2 / Biso mean: 60.7607 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.4→82.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10717 0 164 172 11053
Biso mean--71.62 51.76 -
Num. residues----1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411091
X-RAY DIFFRACTIONf_angle_d0.8815142
X-RAY DIFFRACTIONf_chiral_restr0.031787
X-RAY DIFFRACTIONf_plane_restr0.0041982
X-RAY DIFFRACTIONf_dihedral_angle_d14.5033880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42930.31281240.269125792703100
2.4293-2.460.31781570.2632604276199
2.46-2.49240.29371500.25812608275899
2.4924-2.52650.30051530.262225832736100
2.5265-2.56260.34191350.250425752710100
2.5626-2.60090.28931450.26172585273099
2.6009-2.64150.30991410.256326202761100
2.6415-2.68480.35851410.258426212762100
2.6848-2.73110.30951300.253126552785100
2.7311-2.78080.32841320.259425602692100
2.7808-2.83430.33331390.250126402779100
2.8343-2.89220.28621250.243626082733100
2.8922-2.9550.3051620.251526212783100
2.955-3.02380.28471580.240725732731100
3.0238-3.09940.30311350.238726342769100
3.0994-3.18320.29091300.23582612274299
3.1832-3.27690.24941400.236525952735100
3.2769-3.38270.28571490.23742610275999
3.3827-3.50360.26521500.24032624277499
3.5036-3.64380.28311370.22422579271699
3.6438-3.80970.241280.21942620274899
3.8097-4.01050.26291390.20362608274799
4.0105-4.26180.22061270.18852634276199
4.2618-4.59080.23531340.178526272761100
4.5908-5.05280.19461370.169626482785100
5.0528-5.78370.28891420.20092637277999
5.7837-7.28620.25951450.22372616276199
7.2862-82.6950.27671330.18662688282199
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)
11.55260.04020.48951.05290.17383.12070.10140.0804-0.07930.09430.0635-0.15690.39670.01310.07760.29290.0319-0.0140.2598-0.02420.3874-20.9369-13.2607-20.5507
23.05631.79760.43231.79520.33331.36660.5064-0.6075-0.44750.3007-0.3764-0.07410.0641-0.26440.11510.5946-0.1722-0.07350.5180.07260.4801-15.2698-18.234637.76
31.23980.4940.8860.97770.92933.2154-0.1750.2809-0.1372-0.07870.2746-0.2389-0.19140.39870.08370.528-0.11570.07430.4834-0.02630.472910.93212.87844.948
42.8811.4373-0.08861.886-0.95261.8420.0063-0.7155-0.0692-0.0865-0.1940.1310.3126-0.2784-0.68440.2073-0.00420.09030.41380.0020.296918.6945-7.1456-24.7839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 3:392)A3 - 392
2X-RAY DIFFRACTION2(chain B and resseq 1:392)B1 - 392
3X-RAY DIFFRACTION3(chain C and resseq 3:392)C3 - 392
4X-RAY DIFFRACTION4(chain D and resseq 6:392)D6 - 392

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