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

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Basic information

Entry
Database: PDB / ID: 7rcm
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 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 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: 2.1 Å
Model detailsHuman Galactokinase enzyme with ADP bound
AuthorsWhitby, F.G.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactokinase
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,37717
Polymers84,4062
Non-polymers1,97115
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-76 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.793, 128.793, 240.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Galactokinase / / Galactose kinase


Mass: 42203.020 Da / Num. of mol.: 2 / 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
#3: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / 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 , 6 types, 262 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.41 Å3/Da / Density % sol: 63.96 % / Mosaicity: 0.24 °
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: 2.1→39.82 Å / Num. obs: 68728 / % possible obs: 99.3 % / Redundancy: 16.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.046 / Rrim(I) all: 0.223 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.155.31.1362238341990.5680.5151.2541.292
9.84-39.7631.40.064253948100.9990.0110.06525.498.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUU

1wuu


Resolution: 2.1→39.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.785 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1653 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 3072 4.5 %RANDOM
Rwork0.1957 ---
obs0.1975 65530 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.38 Å2 / Biso mean: 48.471 Å2 / Biso min: 24.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.51 Å20 Å2
2---1.03 Å20 Å2
3---3.34 Å2
Refinement stepCycle: final / Resolution: 2.1→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5900 0 118 249 6267
Biso mean--57.34 48.79 -
Num. residues----782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175708
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6488356
X-RAY DIFFRACTIONr_angle_other_deg1.311.5713195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7265786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8820.311322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05215977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3031562
X-RAY DIFFRACTIONr_chiral_restr0.0720.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021302
LS refinement shellResolution: 2.101→2.156 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.344 203 -
Rwork0.344 4330 -
obs--90.21 %
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)
12.6694-1.04081.07631.3017-0.67541.4843-0.03950.0996-0.0975-0.12230.0237-0.15140.23320.25270.01570.32980.14480.0090.11050.01090.279423.8212-38.57140.6585
21.2408-0.27860.4493.2123-1.40342.27790.1864-0.1579-0.1327-0.05520.05820.49670.6235-0.0302-0.24460.28710.01-0.13680.03-0.00740.30734.8067-29.625428.9216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 401
2X-RAY DIFFRACTION2B2 - 401

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