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- PDB-3nca: X-ray structure of ketohexokinase in complex with a thieno pyridi... -

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Basic information

Entry
Database: PDB / ID: 3nca
TitleX-ray structure of ketohexokinase in complex with a thieno pyridinol compound
ComponentsKetohexokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion ...Essential fructosuria / ketohexokinase / ketohexokinase activity / fructose binding / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ketohexokinase / : / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
thieno[3,2-b]pyridin-7-ol / Ketohexokinase / Isoform A of Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsAbad, M.C. / Gibbs, A.C. / Spurlino, J.C.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Electron density guided fragment-based lead discovery of ketohexokinase inhibitors.
Authors: Gibbs, A.C. / Abad, M.C. / Zhang, X. / Tounge, B.A. / Lewandowski, F.A. / Struble, G.T. / Sun, W. / Sui, Z. / Kuo, L.C.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2017Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5936
Polymers68,1532
Non-polymers4394
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-64 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.942, 85.539, 137.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ketohexokinase / Hepatic fructokinase


Mass: 34076.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Plasmid: pET28s / Production host: Escherichia coli (E. coli)
References: UniProt: P50053-2, UniProt: P50053*PLUS, ketohexokinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TR2 / thieno[3,2-b]pyridin-7-ol


Mass: 151.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NOS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 17% PEG 8K, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 3, 2007 / Details: mirrors
RadiationMonochromator: double crystal mono Si(111) from accel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 30467 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.061 / Net I/σ(I): 21
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
JDirectordata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3NBV

3nbv


Resolution: 2.602→40.84 Å / SU ML: 0.34 / Isotropic thermal model: anisotropic / σ(F): 0.13 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 1872 6.51 %
Rwork0.1922 --
obs0.1953 28757 93.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.561 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0574 Å2-0 Å20 Å2
2---1.6652 Å2-0 Å2
3---2.7227 Å2
Refinement stepCycle: LAST / Resolution: 2.602→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 25 91 4671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094663
X-RAY DIFFRACTIONf_angle_d1.1746311
X-RAY DIFFRACTIONf_dihedral_angle_d15.7631704
X-RAY DIFFRACTIONf_chiral_restr0.072698
X-RAY DIFFRACTIONf_plane_restr0.005834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6024-2.67280.36831070.32821638X-RAY DIFFRACTION76
2.6728-2.75140.26571270.24851816X-RAY DIFFRACTION84
2.7514-2.84020.29391350.21451977X-RAY DIFFRACTION91
2.8402-2.94170.28041410.22312017X-RAY DIFFRACTION93
2.9417-3.05940.29621430.22642091X-RAY DIFFRACTION95
3.0594-3.19860.31361470.22352097X-RAY DIFFRACTION97
3.1986-3.36710.26521480.20532137X-RAY DIFFRACTION98
3.3671-3.5780.28741580.19572115X-RAY DIFFRACTION97
3.578-3.85410.2351440.18412148X-RAY DIFFRACTION97
3.8541-4.24160.21621490.16332147X-RAY DIFFRACTION97
4.2416-4.85450.15511540.14162197X-RAY DIFFRACTION99
4.8545-6.11280.19521530.16682231X-RAY DIFFRACTION98
6.1128-40.84520.21761660.17322274X-RAY DIFFRACTION97

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