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- PDB-3nbv: X-ray Structure of Ketohexokinase in complex with AMP-PNP and fructose -

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Basic information

Entry
Database: PDB / ID: 3nbv
TitleX-ray Structure of Ketohexokinase in complex with AMP-PNP and fructose
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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / beta-D-fructofuranose / Ketohexokinase / Isoform A of Ketohexokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAbad, M.C. / Gibbs, A.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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)69,4426
Polymers68,1532
Non-polymers1,2894
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-30 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.845, 86.035, 136.961
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 65.65 %
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: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2007 / Details: mirror
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: 2.2→50 Å / Num. obs: 49441 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.066 / Net I/σ(I): 18.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.85 / Num. unique all: 4843 / % possible all: 97.8

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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 2HLZ

2hlz


Resolution: 2.3→41.041 Å / SU ML: 0.32 / Isotropic thermal model: anisotropic / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1754 4.04 %random
Rwork0.206 ---
obs0.2073 43397 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.236 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5427 Å20 Å2-0 Å2
2--9.173 Å20 Å2
3----4.6303 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 79 120 4754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084722
X-RAY DIFFRACTIONf_angle_d1.0966406
X-RAY DIFFRACTIONf_dihedral_angle_d17.4831794
X-RAY DIFFRACTIONf_chiral_restr0.067710
X-RAY DIFFRACTIONf_plane_restr0.005835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.32181390.26173128X-RAY DIFFRACTION98
2.3622-2.43170.30011230.2563167X-RAY DIFFRACTION98
2.4317-2.51020.32461410.2473174X-RAY DIFFRACTION99
2.5102-2.59990.27791350.2373184X-RAY DIFFRACTION99
2.5999-2.7040.2421340.22723161X-RAY DIFFRACTION99
2.704-2.8270.2551310.21753209X-RAY DIFFRACTION99
2.827-2.9760.32671310.22333211X-RAY DIFFRACTION99
2.976-3.16240.2551360.22453204X-RAY DIFFRACTION99
3.1624-3.40640.23071380.20943251X-RAY DIFFRACTION100
3.4064-3.7490.20571400.18423262X-RAY DIFFRACTION100
3.749-4.2910.19721370.17793276X-RAY DIFFRACTION100
4.291-5.40430.18671400.1653304X-RAY DIFFRACTION99
5.4043-41.04730.25091290.2123112X-RAY DIFFRACTION90

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