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- PDB-7rcl: Crystal Structure of ADP-bound Galactokinase -

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Basic information

Entry
Database: PDB / ID: 7rcl
TitleCrystal Structure of ADP-bound Galactokinase
ComponentsGalactokinase
KeywordsSUGAR BINDING PROTEIN / GALK / galactokinase / Galactose / ADP / disulfide
Function / homology
Function and homology information


glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose catabolic process via UDP-galactose, Leloir pathway / galactose binding / galactose metabolic process / extracellular exosome ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose catabolic process via UDP-galactose, Leloir pathway / galactose binding / galactose metabolic process / 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 N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / alpha-D-galactopyranose / PHOSPHATE ION / Galactokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Model detailsHuman Galactokinase enzyme with ADP bound
AuthorsWhitby, F.G. / Hall, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1HD074844 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors.
Authors: Liu, L. / Tang, M. / Pragani, R. / Whitby, F.G. / Zhang, Y.Q. / Balakrishnan, B. / Fang, Y. / Karavadhi, S. / Tao, D. / LeClair, C.A. / Hall, M.D. / Marugan, J.J. / Boxer, M. / Shen, M. / ...Authors: Liu, L. / Tang, M. / Pragani, R. / Whitby, F.G. / Zhang, Y.Q. / Balakrishnan, B. / Fang, Y. / Karavadhi, S. / Tao, D. / LeClair, C.A. / Hall, M.D. / Marugan, J.J. / Boxer, M. / Shen, M. / Hill, C.P. / Lai, K. / Patnaik, S.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)172,47531
Polymers168,8124
Non-polymers3,66327
Water7,152397
1
A: Galactokinase
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,19015
Polymers84,4062
Non-polymers1,78413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,28516
Polymers84,4062
Non-polymers1,87914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.901, 114.126, 206.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Galactokinase / Galactose kinase


Mass: 42203.020 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 / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P51570, galactokinase
#2: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 420 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.39 Å3/Da / Density % sol: 63.67 % / Mosaicity: 0.518 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Seeding into drops containing GALK protein at 8 mg/ml, 2.3M Na/K pH6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1533 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1533 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 86404 / % possible obs: 95.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.069 / Rrim(I) all: 0.222 / Χ2: 1.216 / Net I/σ(I): 9 / Num. measured all: 955737
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.496.185200.3560.7971.26595
2.49-2.596.484860.4310.7231.27895.3
2.59-2.76.884770.5540.6251.24395.1
2.7-2.857.584670.6740.5161.24594.6
2.85-3.02884560.7690.3621.17894.30.953
3.02-3.268.784230.890.2431.24593.60.6810.726
3.26-3.581184130.9630.1481.18993.60.5020.525
3.58-4.11585670.9830.0841.34694.80.3310.342
4.1-5.1720.191360.9910.0511.19699.90.2230.23
5.17-5019.294590.9980.0251.1171000.1070.11

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wuu

1wuu


Resolution: 2.4→39.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.248 / SU ML: 0.178 / SU R Cruickshank DPI: 0.2564 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1726 2 %RANDOM
Rwork0.1732 ---
obs0.1743 84573 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.74 Å2 / Biso mean: 56.893 Å2 / Biso min: 30.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2--2.51 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.4→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11800 0 219 397 12416
Biso mean--68.48 54.92 -
Num. residues----1564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01312354
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711462
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.64816806
X-RAY DIFFRACTIONr_angle_other_deg1.4161.56926503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.77651582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16620.368653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61715125
X-RAY DIFFRACTIONr_chiral_restr0.0870.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022622
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 124 -
Rwork0.278 6093 -
all-6217 -
obs--94.33 %
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)
10.8948-0.0228-0.28560.11960.22070.59170.02050.2652-0.01690.0581-0.011-0.0291-0.0171-0.1137-0.00950.14540.0354-0.04660.3195-0.00230.032921.0799-26.7385-5.9596
20.33140.1422-0.05030.1865-0.31870.8678-0.05110.01450.05840.05050.01930.0042-0.0185-0.07640.03180.20630.039-0.01610.2150.02650.053115.8466-32.131748.1
30.008-0.0041-0.04040.4410.80031.82380.01660.02330.00280.11550.0876-0.01150.30440.1697-0.10420.22020.0764-0.03040.2805-0.06220.031922.9339-61.6998-0.9639
40.44520.3684-0.24480.4901-0.43081.11850.08890.03540.02490.3127-0.15390.0117-0.32920.12550.0650.4206-0.1697-0.04040.202-0.01370.021836.8722-4.460844.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 401
2X-RAY DIFFRACTION2B2 - 401
3X-RAY DIFFRACTION3C2 - 401
4X-RAY DIFFRACTION4D2 - 401

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