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- PDB-6q8z: Structure of human galactokinase 1 bound with N-(Cyclobutylmethyl... -

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Basic information

Entry
Database: PDB / ID: 6q8z
TitleStructure of human galactokinase 1 bound with N-(Cyclobutylmethyl)-1,5-dimethyl-1H-pyrazole-4-carboxamide
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 catabolism / galactose binding / galactose metabolic process / galactose catabolic process via UDP-galactose / extracellular exosome ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose binding / galactose metabolic process / galactose catabolic process via UDP-galactose / 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-HR5 / 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 N-(Cyclobutylmethyl)-1,5-dimethyl-1H-pyrazole-4-carboxamide
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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,51813
Polymers169,3044
Non-polymers2,2149
Water13,313739
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0644
Polymers42,3261
Non-polymers7383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8573
Polymers42,3261
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2715
Polymers42,3261
Non-polymers9454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactokinase


Theoretical massNumber of molelcules
Total (without water)42,3261
Polymers42,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.624, 114.393, 120.853
Angle α, β, γ (deg.)90.000, 100.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 393
211chain BB3 - 393
311chain CC3 - 393
411chain DD8 - 392

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Components

#1: Protein
Galactokinase / Galactose kinase


Mass: 42326.109 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-HR5 / ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide


Mass: 207.272 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17N3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M MOPS/sodium HEPES pH7-7.5, 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 pH7-7.5, 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 and 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: 1.81→82.41 Å / Num. obs: 178777 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Net I/σ(I): 11.5 / Num. measured all: 600183 / Scaling rejects: 353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.81-1.863.20.877131660.7270.5691.04999.9
8.09-82.413.50.01620690.9990.010.01999.5

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Processing

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

1wuu


Resolution: 2.4→52.737 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.69 / Details: Data cut to 2.4A
RfactorNum. reflection% reflection
Rfree0.2834 8845 4.96 %
Rwork0.2409 --
obs0.2431 178200 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.96 Å2 / Biso mean: 47.0671 Å2 / Biso min: 21.76 Å2
Refinement stepCycle: final / Resolution: 2.4→52.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10954 0 159 739 11852
Biso mean--46.85 51.51 -
Num. residues----1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711338
X-RAY DIFFRACTIONf_angle_d1.69715475
X-RAY DIFFRACTIONf_chiral_restr0.0961820
X-RAY DIFFRACTIONf_plane_restr0.012058
X-RAY DIFFRACTIONf_dihedral_angle_d14.8294001
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6582X-RAY DIFFRACTION6.726TORSIONAL
12B6582X-RAY DIFFRACTION6.726TORSIONAL
13C6582X-RAY DIFFRACTION6.726TORSIONAL
14D6582X-RAY DIFFRACTION6.726TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4561-2.52840.28643040.25315658
2.5284-2.610.29742960.25315631
2.61-2.70330.31322990.25975667
2.7033-2.81150.3192870.25795672
2.8115-2.93940.32443100.25565665
2.9394-3.09440.28873170.25455652
3.0944-3.28820.3032750.25175663
3.2882-3.54210.27663400.24295652
3.5421-3.89840.26812820.22445710
3.8984-4.46230.23623270.19515657
4.4623-5.6210.21112910.18415725
5.621-52.7150.23653080.19815780
Refinement TLS params.Method: refined / Origin x: -2.2143 Å / Origin y: -5.7829 Å / Origin z: 9.8475 Å
111213212223313233
T0.3463 Å2-0.0557 Å2-0.0067 Å2-0.2732 Å2-0.0095 Å2--0.3275 Å2
L0.141 °20.0152 °20.2054 °2-0.0193 °2-0.0455 °2--0.7131 °2
S0.0807 Å °-0.0653 Å °-0.0521 Å °0.0643 Å °-0.0278 Å °-0.0269 Å °0.0522 Å °-0.0581 Å °-0.0439 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allE1 - 3
2X-RAY DIFFRACTION1allA1 - 393
3X-RAY DIFFRACTION1allB3 - 393
4X-RAY DIFFRACTION1allC3 - 393
5X-RAY DIFFRACTION1allD8 - 392
6X-RAY DIFFRACTION1allF1 - 3
7X-RAY DIFFRACTION1allS1 - 745

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