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- PDB-6etj: HUMAN PFKFB3 IN COMPLEX WITH KAN0438241 -

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Basic information

Entry
Database: PDB / ID: 6etj
TitleHUMAN PFKFB3 IN COMPLEX WITH KAN0438241
Components6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
KeywordsANTITUMOR PROTEIN / DNA damage repair / homologous recombination / glycolysis / nucleotide metabolism / PFKFB3
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 / fructose metabolic 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 / Chem-BWW / 6-O-phosphono-beta-D-fructofuranose / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.51 Å
AuthorsGustafsson, N.M.S. / Lundback, T. / Farnegardh, K. / Groth, P. / Wiitta, E. / Jonsson, M. / Hallberg, K. / Pennisi, R. / Huguet Ninou, A. / Martinsson, J. ...Gustafsson, N.M.S. / Lundback, T. / Farnegardh, K. / Groth, P. / Wiitta, E. / Jonsson, M. / Hallberg, K. / Pennisi, R. / Huguet Ninou, A. / Martinsson, J. / Norstrom, C. / Schultz, J. / Andersson, M. / Markova, N. / Marttila, P. / Norin, M. / Olin, T. / Helleday, T.
CitationJournal: Nat Commun / Year: 2018
Title: Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination.
Authors: Gustafsson, N.M.S. / Farnegardh, K. / Bonagas, N. / Ninou, A.H. / Groth, P. / Wiita, E. / Jonsson, M. / Hallberg, K. / Lehto, J. / Pennisi, R. / Martinsson, J. / Norstrom, C. / Hollers, J. / ...Authors: Gustafsson, N.M.S. / Farnegardh, K. / Bonagas, N. / Ninou, A.H. / Groth, P. / Wiita, E. / Jonsson, M. / Hallberg, K. / Lehto, J. / Pennisi, R. / Martinsson, J. / Norstrom, C. / Hollers, J. / Schultz, J. / Andersson, M. / Markova, N. / Marttila, P. / Kim, B. / Norin, M. / Olin, T. / Helleday, T.
History
DepositionOct 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 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

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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)60,9425
Polymers59,7731
Non-polymers1,1694
Water1,838102
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)121,88410
Polymers119,5462
Non-polymers2,3388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Unit cell
Length a, b, c (Å)103.774, 103.774, 259.563
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 59773.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKFB3 / Plasmid: pDest14 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q16875, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase
#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose


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 , 4 types, 105 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BWW / 4-[[3-(5-fluoranyl-2-oxidanyl-phenyl)phenyl]sulfonylamino]-2-oxidanyl-benzoic acid


Mass: 403.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14FNO6S / Feature type: SUBJECT OF INVESTIGATION
#5: 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.: 102 / 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: 4.01 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG3350, Hepes, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.51→34.28 Å / Num. obs: 29050 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.128 % / Biso Wilson estimate: 47.566 Å2 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.111 / Χ2: 0.993 / Net I/σ(I): 11.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.51-2.584.2610.7531.921010.86399.9
2.58-2.654.2190.5572.4720670.639100
2.65-2.724.2660.492.8820030.56199.9
2.72-2.814.2310.4043.4319350.46399.8
2.81-2.94.1950.3224.2818880.3799.8
2.9-34.2680.2565.3918160.29399.8
3-3.114.1950.26.6217620.2399.8
3.11-3.244.1970.1647.9517040.18899.8
3.24-3.384.2180.12410.5416370.14399.8
3.38-3.554.1180.0913.5615730.10499.9
3.55-3.744.1510.0815.3315040.09299.5
3.74-3.974.1030.06518.2114260.07499.8
3.97-4.244.060.05321.2213310.06199.6
4.24-4.584.0920.05122.8412710.05899.6
4.58-5.023.9420.04424.4711640.05199
5.02-5.613.9620.04922.8610650.05799.6
5.61-6.483.9570.04922.59590.05799.3
6.48-7.943.7470.0424.028150.04698.3
7.94-11.233.6540.02932.26480.03497.4
11.23-34.283.150.02731.13810.03291.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.22data extraction
XSCALEdata reduction
RefinementResolution: 2.51→34.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.626 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.221
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1453 5 %RANDOM
Rwork0.1921 ---
obs0.1943 27596 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.9 Å2 / Biso mean: 42.154 Å2 / Biso min: 16.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.69 Å20 Å2
2--1.37 Å2-0 Å2
3----2.06 Å2
Refinement stepCycle: final / Resolution: 2.51→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 75 102 3708
Biso mean--45.62 37.31 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023714
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9935041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33423.352182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48215663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8451535
X-RAY DIFFRACTIONr_chiral_restr0.0970.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212804
LS refinement shellResolution: 2.51→2.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 96 -
Rwork0.287 1750 -
all-1846 -
obs--99.89 %

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