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- PDB-3qpv: PFKFB3 trapped in a phospho-enzyme intermediate state -

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Basic information

Entry
Database: PDB / ID: 3qpv
TitlePFKFB3 trapped in a phospho-enzyme intermediate state
Components6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
KeywordsTRANSFERASE / HYDROLASE / kinase/bisphosphatase
Function / homology
Function and homology information


6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / glial cell differentiation / fructose metabolic process / motor behavior / glycolytic process ...6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / glial cell differentiation / fructose metabolic process / motor behavior / glycolytic process / apoptotic process / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily ...Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / 2,6-di-O-phosphono-beta-D-fructofuranose / PHOSPHONIC ACID / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCavalier, M.C. / Kim, S.G. / Neau, D. / Lee, Y.H.
CitationJournal: Proteins / Year: 2012
Title: Molecular basis of the fructose-2,6-bisphosphatase reaction of PFKFB3: Transition state and the C-terminal function.
Authors: Cavalier, M.C. / Kim, S.G. / Neau, D. / Lee, Y.H.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8045
Polymers59,6941
Non-polymers1,1094
Water3,153175
1
A: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
hetero molecules

A: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,60710
Polymers119,3882
Non-polymers2,2198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)102.146, 102.146, 259.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 6PF-2-K/Fru-2 / 6-P2ase 3 / PFK/FBPase 3 / 6PF-2-K/Fru-2 / 6-P2ase brain/placenta-type isozyme / ...6PF-2-K/Fru-2 / 6-P2ase 3 / PFK/FBPase 3 / 6PF-2-K/Fru-2 / 6-P2ase brain/placenta-type isozyme / Renal carcinoma antigen NY-REN-56 / iPFK-2 / 6-phosphofructo-2-kinase / Fructose-2 / 6-bisphosphatase


Mass: 59694.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKFB3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16875, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-FDP / 2,6-di-O-phosphono-beta-D-fructofuranose / FRUCTOSE-2,6-DIPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructose / 2,6-di-O-phosphono-D-fructose / 2,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf2PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 177 molecules

#3: Chemical ChemComp-PHS / PHOSPHONIC ACID


Mass: 81.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O3P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HCl,20-25% ethylene glycol, 200-400mM Tartaric Acid, 5% glycerol, and 12% polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.3808 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2007
RadiationMonochromator: Si(111) Channel Cut Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3808 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 30381 / Num. obs: 30381 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.45→2.54 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.164 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 2741 10 %RANDOM
Rwork0.1937 ---
obs0.19916 24542 95.43 %-
all-30381 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3597 0 67 175 3839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223749
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1791.9845080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86723.441186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83415669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4461535
X-RAY DIFFRACTIONr_chiral_restr0.1430.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.21903
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22547
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3461.52281
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20123588
X-RAY DIFFRACTIONr_scbond_it3.35731678
X-RAY DIFFRACTIONr_scangle_it5.1484.51491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 183 -
Rwork0.261 1610 -
obs--87.08 %

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