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- PDB-3pfk: PHOSPHOFRUCTOKINASE. STRUCTURE AND CONTROL -

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Entry
Database: PDB / ID: 3pfk
TitlePHOSPHOFRUCTOKINASE. STRUCTURE AND CONTROL
ComponentsPHOSPHOFRUCTOKINASE
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsEvans, P.R. / Hudson, P.J.
Citation
Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: Phosphofructokinase: structure and control.
Authors: Evans, P.R. / Farrants, G.W. / Hudson, P.J.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Unliganded Phosphofructokinase from Escherichia Coli
Authors: Rypniewski, W.R. / Evans, P.R.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of the Complex of Phosphofructokinase from Escherichia Coli with its Reaction Products
Authors: Shirakihara, Y. / Evans, P.R.
#3: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallographic Structure of Allosterically Inhibited Phosphofructokinase at 7 Angstroms Resolution
Authors: Evans, P.R. / Farrants, G.W. / Lawrence, M.C.
#4: Journal: Eur.J.Biochem. / Year: 1985
Title: Nucleotide Sequence and High-Level Expression of the Major Escherichia Coli Phosphofructokinase
Authors: Hellinga, H.W. / Evans, P.R.
#5: Journal: Nature / Year: 1979
Title: Structure and Control of Phosphofructokinase from Bacillus Stearothermophilus
Authors: Evans, P.R. / Hudson, P.J.
#6: Journal: Proc.FEBS Meet. / Year: 1978
Title: The Three-Dimensional Structure of Phosphofructokinase from Bacillus Stearothermophilus
Authors: Evans, P.R. / Hudson, P.J.
History
DepositionJan 25, 1988Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3573
Polymers34,1671
Non-polymers1902
Water1,63991
1
A: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,42712
Polymers136,6674
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area15240 Å2
ΔGint-97 kcal/mol
Surface area39970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.500, 84.100, 61.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

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Components

#1: Protein PHOSPHOFRUCTOKINASE


Mass: 34166.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: 293 / Strain (production host): 293 / References: UniProt: P00512, 6-phosphofructokinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal grow
*PLUS
pH: 7.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mpotassium phosphate11
22 mMF6P11

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→30 Å / Rfactor obs: 0.171
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 10 91 2462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.037

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