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- PDB-9cxo: Crystal structure of Human FN3K(D217S) mutant bound with ATP -

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Basic information

Entry
Database: PDB / ID: 9cxo
TitleCrystal structure of Human FN3K(D217S) mutant bound with ATP
ComponentsFructosamine-3-kinase
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


protein-fructosamine 3-kinase / fructosamine metabolic process / fructoselysine metabolic process / protein deglycation / protein-fructosamine 3-kinase activity / protein-ribulosamine 3-kinase / protein-ribulosamine 3-kinase activity / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / epithelial cell differentiation / post-translational protein modification ...protein-fructosamine 3-kinase / fructosamine metabolic process / fructoselysine metabolic process / protein deglycation / protein-fructosamine 3-kinase activity / protein-ribulosamine 3-kinase / protein-ribulosamine 3-kinase activity / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / epithelial cell differentiation / post-translational protein modification / kinase activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
Fructosamine/Ketosamine-3-kinase / Fructosamine kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Fructosamine-3-kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGarg, A. / On, K.F. / Joshua-tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2025
Title: The molecular basis of Human FN3K mediated phosphorylation of glycated substrates.
Authors: Garg, A. / On, K.F. / Xiao, Y. / Elkayam, E. / Cifani, P. / David, Y. / Joshua-Tor, L.
History
DepositionJul 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructosamine-3-kinase
B: Fructosamine-3-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,10118
Polymers65,9612
Non-polymers2,13916
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-45 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.312, 112.448, 132.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructosamine-3-kinase / Protein-psicosamine 3-kinase FN3K / Protein-ribulosamine 3-kinase FN3K


Mass: 32980.730 Da / Num. of mol.: 2 / Mutation: D217S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN3K / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H479, protein-fructosamine 3-kinase, protein-ribulosamine 3-kinase

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Non-polymers , 6 types, 189 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 58.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 6000, 0.1 M HEPES pH 7.5, and 0.175 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2022
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.32→132.9 Å / Num. obs: 34801 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12
Reflection shellResolution: 2.32→2.43 Å / Rmerge(I) obs: 0.677 / Num. unique obs: 3417 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487-0000refinement
Cootmodel building
RAPDdata processing
PHASERphasing
RAPDdata reduction
RAPDdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→85.85 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 1731 4.98 %
Rwork0.2005 --
obs0.2024 34739 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→85.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 129 173 4899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024838
X-RAY DIFFRACTIONf_angle_d0.5656544
X-RAY DIFFRACTIONf_dihedral_angle_d7.127658
X-RAY DIFFRACTIONf_chiral_restr0.062674
X-RAY DIFFRACTIONf_plane_restr0.004839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.28931400.2522645X-RAY DIFFRACTION96
2.38-2.460.31621300.23692683X-RAY DIFFRACTION100
2.46-2.550.26051410.23232691X-RAY DIFFRACTION99
2.55-2.650.26351360.2252751X-RAY DIFFRACTION100
2.65-2.770.28141300.2262740X-RAY DIFFRACTION100
2.77-2.920.26471540.21752738X-RAY DIFFRACTION100
2.92-3.10.22281550.22412740X-RAY DIFFRACTION100
3.1-3.340.27711200.21212767X-RAY DIFFRACTION100
3.34-3.680.2291590.19072718X-RAY DIFFRACTION99
3.68-4.210.21361580.17332777X-RAY DIFFRACTION100
4.21-5.30.21341590.17112822X-RAY DIFFRACTION100
5.3-85.850.22571490.20432936X-RAY DIFFRACTION99

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