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- PDB-6q91: Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl... -

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Basic information

Entry
Database: PDB / ID: 6q91
TitleStructure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide
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 / L-arabinokinase activity / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose catabolic process via UDP-galactose / galactose metabolic process ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / L-arabinokinase activity / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose catabolic process via UDP-galactose / galactose metabolic process / galactose binding / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
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-HR8 / 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 5-Chloro-N-isobutyl-2-methoxybenzamide
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 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)171,39814
Polymers168,8404
Non-polymers2,55910
Water5,855325
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9824
Polymers42,2101
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9824
Polymers42,2101
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9824
Polymers42,2101
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4522
Polymers42,2101
Non-polymers2421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.323, 114.959, 120.918
Angle α, β, γ (deg.)90.000, 100.790, 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 / Mutation: K252A, E253A
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


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-HR8 / 5-chloranyl-2-methoxy-~{N}-(2-methylpropyl)benzamide


Mass: 241.714 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16ClNO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 58.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MOPS/sodium HEPES, 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 ...Details: 0.1M MOPS/sodium HEPES, 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 actetate, 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: 2.27→82.74 Å / Num. obs: 91197 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.131 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.27-2.393.51.393133670.6160.8731.64899.9
7.16-82.613.40.03329480.9980.0210.0499.2

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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→82.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.165 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.277
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 3787 4.9 %RANDOM
Rwork0.2159 ---
obs0.2193 72868 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.38 Å2 / Biso mean: 44.518 Å2 / Biso min: 15.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-2.59 Å2
2--4.41 Å2-0 Å2
3----3.4 Å2
Refinement stepCycle: final / Resolution: 2.4→82.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11006 0 178 325 11509
Biso mean--58.96 41.4 -
Num. residues----1536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311395
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710374
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.65315542
X-RAY DIFFRACTIONr_angle_other_deg1.3221.57723877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.251526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86620.99505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.469151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1391583
X-RAY DIFFRACTIONr_chiral_restr0.0670.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022330
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 277 -
Rwork0.322 5409 -
all-5686 -
obs--99.84 %

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