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- PDB-3q92: X-ray Structure of ketohexokinase in complex with a pyrimidopyrim... -

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Basic information

Entry
Database: PDB / ID: 3q92
TitleX-ray Structure of ketohexokinase in complex with a pyrimidopyrimidine analog 1
ComponentsKetohexokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / ATP Binding / 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 / cytosol / cytoplasm
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
Chem-XNB / Ketohexokinase / Isoform A of Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAbad, M.C.
CitationJournal: ACS Med Chem Lett / Year: 2011
Title: Inhibitors of Ketohexokinase: Discovery of Pyrimidinopyrimidines with Specific Substitution that Complements the ATP-Binding Site.
Authors: Maryanoff, B.E. / O'Neill, J.C. / McComsey, D.F. / Yabut, S.C. / Luci, D.K. / Jordan, A.D. / Masucci, J.A. / Jones, W.J. / Abad, M.C. / Gibbs, A.C. / Petrounia, I.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2867
Polymers68,1532
Non-polymers1,1335
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-66 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.880, 86.073, 136.650
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-XNB / N~8~-(cyclopropylmethyl)-N~4~-[2-(methylsulfanyl)phenyl]-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine


Mass: 422.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N8S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 65.6 %
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-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 21, 2008 / 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: 2.5→44.96 Å / Num. all: 34751 / Num. obs: 31943 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.16 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3437 / % possible all: 91.9

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Processing

Software
NameVersionClassification
JDirectordata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NBV

3nbv


Resolution: 2.8→26.757 Å / SU ML: 0.52 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1967 8.92 %random
Rwork0.2015 ---
obs0.207 22052 89.28 %-
all-22052 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.577 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8568 Å20 Å20 Å2
2---1.3376 Å2-0 Å2
3---5.1944 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 75 50 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094727
X-RAY DIFFRACTIONf_angle_d1.2246401
X-RAY DIFFRACTIONf_dihedral_angle_d17.3911733
X-RAY DIFFRACTIONf_chiral_restr0.074699
X-RAY DIFFRACTIONf_plane_restr0.005839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87010.37751340.26871389X-RAY DIFFRACTION87
2.8701-2.94760.33151550.25651369X-RAY DIFFRACTION89
2.9476-3.03420.36791230.25531417X-RAY DIFFRACTION89
3.0342-3.1320.31131410.24941446X-RAY DIFFRACTION90
3.132-3.24370.37281490.24251417X-RAY DIFFRACTION91
3.2437-3.37340.37771410.2291465X-RAY DIFFRACTION92
3.3734-3.52660.29211500.20911453X-RAY DIFFRACTION91
3.5266-3.71210.2441390.18531467X-RAY DIFFRACTION92
3.7121-3.94390.22121460.17761452X-RAY DIFFRACTION91
3.9439-4.24740.21821450.16151452X-RAY DIFFRACTION91
4.2474-4.67270.20131360.14241467X-RAY DIFFRACTION91
4.6727-5.34420.1991420.14581464X-RAY DIFFRACTION90
5.3442-6.71550.23171320.17711462X-RAY DIFFRACTION88
6.7155-26.75840.19871340.17381365X-RAY DIFFRACTION79

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