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- PDB-3qa2: X-ray Structure of ketohexokinase in complex with a pyrimidopyrim... -

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Basic information

Entry
Database: PDB / ID: 3qa2
TitleX-ray Structure of ketohexokinase in complex with a pyrimidopyrimidine analog 2
ComponentsKetohexokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / ATP Binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / ketohexokinase activity / 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 / extracellular exosome / ATP 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-XNA / Ketohexokinase / Isoform A of Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.519 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 10, 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

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2227
Polymers68,1532
Non-polymers1,0695
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-68 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.851, 86.546, 137.453
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-XNA / N~8~-(cyclopropylmethyl)-N~4~-(2-methylphenyl)-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine


Mass: 390.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.62 Å3/Da / Density % sol: 65.98 %
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: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 33903 / Num. obs: 31612 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2701 / Rsym value: 0.367 / % possible all: 81.5

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Processing

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

3nbv


Resolution: 2.519→31.741 Å / SU ML: 0.29 / Isotropic thermal model: anisotropic / σ(F): 0.07 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1898 6.13 %random
Rwork0.1956 ---
obs0.1981 30948 90.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.237 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.8645 Å20 Å20 Å2
2--2.8656 Å2-0 Å2
3---6.9989 Å2
Refinement stepCycle: LAST / Resolution: 2.519→31.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 73 8 4647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084729
X-RAY DIFFRACTIONf_angle_d1.1876402
X-RAY DIFFRACTIONf_dihedral_angle_d16.1211744
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 (%)
2.519-2.58190.3196810.2791311X-RAY DIFFRACTION58
2.5819-2.65170.30951050.26951593X-RAY DIFFRACTION71
2.6517-2.72970.31291150.2781807X-RAY DIFFRACTION80
2.7297-2.81770.30561340.24351965X-RAY DIFFRACTION88
2.8177-2.91840.29921380.25272088X-RAY DIFFRACTION92
2.9184-3.03510.28881410.2492143X-RAY DIFFRACTION95
3.0351-3.17320.27181340.24312183X-RAY DIFFRACTION96
3.1732-3.34030.28921460.23632215X-RAY DIFFRACTION97
3.3403-3.54930.26211430.20692205X-RAY DIFFRACTION97
3.5493-3.82290.24221450.18922237X-RAY DIFFRACTION98
3.8229-4.20690.19881570.18062249X-RAY DIFFRACTION98
4.2069-4.81380.20561470.15372318X-RAY DIFFRACTION100
4.8138-6.0580.22061490.17692324X-RAY DIFFRACTION100
6.058-31.74390.19611630.16352412X-RAY DIFFRACTION99

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