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- PDB-6q90: Structure of human galactokinase 1 bound with 1-(4-Methoxyphenyl)... -

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Basic information

Entry
Database: PDB / ID: 6q90
TitleStructure of human galactokinase 1 bound with 1-(4-Methoxyphenyl)-3-(4-pyridinyl)urea
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 / N-(4-methoxyphenyl)-N'-pyridin-4-ylurea / Galactokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 1-(4-Methoxyphenyl)-3-(4-pyridinyl)urea
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
DepositionDec 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 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)170,91812
Polymers168,8404
Non-polymers2,0788
Water4,161231
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7413
Polymers42,2101
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7413
Polymers42,2101
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9844
Polymers42,2101
Non-polymers7743
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)73.550, 114.510, 120.810
Angle α, β, γ (deg.)90.000, 100.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Galactokinase / / Galactose kinase


Mass: 42209.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Production host: Escherichia coli (E. coli) / 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
#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-JHJ / N-(4-methoxyphenyl)-N'-pyridin-4-ylurea


Mass: 243.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13N3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MOPS/sodium HEPES, pH 7-7.5; 40-50% morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M morpheus carboxylic acids mix (0.02M each of: sodium formate, ...Details: 0.1M MOPS/sodium HEPES, pH 7-7.5; 40-50% morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M morpheus carboxylic acids mix (0.02M each of: sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium oxamate, potassium sodium tartrate tetrahydrate
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: 2.08→67.41 Å / Num. obs: 117782 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 10.6 / Num. measured all: 398892 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.08-2.133.21.06186830.6270.6961.27399.7
9.3-67.413.50.02113340.9990.0130.02597

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wuu

1wuu


Resolution: 2.4→67.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.175 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.267
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 3872 5 %RANDOM
Rwork0.2201 ---
obs0.223 72964 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.2 Å2 / Biso mean: 43.633 Å2 / Biso min: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å2-2.14 Å2
2--2.33 Å20 Å2
3----2.7 Å2
Refinement stepCycle: final / Resolution: 2.4→67.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10954 0 150 231 11335
Biso mean--56.03 40.96 -
Num. residues----1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311330
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710267
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.65715471
X-RAY DIFFRACTIONr_angle_other_deg1.3181.58123593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.38220.856479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.291151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7961580
X-RAY DIFFRACTIONr_chiral_restr0.0910.21541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022340
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 296 -
Rwork0.272 5396 -
all-5692 -
obs--99.86 %

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