Structure of phosphofructokinase from rabbit skeletal muscle

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

Starting Model: experimental
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The Crystal Structures of Eukaryotic Phosphofructokinases from Baker's Yeast and Rabbit Skeletal Muscle.

Banaszak, K.Mechin, I.Obmolova, G.Oldham, M.Chang, S.H.Ruiz, T.Radermacher, M.Kopperschlager, G.Rypniewski, W.

(2011) J Mol Biol 407: 284-297

  • DOI: https://doi.org/10.1016/j.jmb.2011.01.019
  • Primary Citation of Related Structures:  
    3O8L, 3O8N, 3O8O

  • PubMed Abstract: 

    Phosphofructokinase 1 (PFK) is a multisubunit allosteric enzyme that catalyzes the principal regulatory step in glycolysis-the phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate by ATP. The activity of eukaryotic PFK is modulated by a number of effectors in response to the cell's needs for energy and building blocks for biosynthesis. The crystal structures of eukaryotic PFKs-from Saccharomyces cerevisiae and rabbit skeletal muscle-demonstrate how successive gene duplications and fusion are reflected in the protein structure and how they allowed the evolution of new functionalities. The basic framework inherited from prokaryotes is conserved, and additional levels of structural and functional complexity have evolved around it. Analysis of protein-ligand complexes has shown how PFK is activated by fructose 2,6-bisphosphate (a powerful PFK effector found only in eukaryotes) and reveals a novel nucleotide binding site. Crystallographic results have been used as the basis for structure-based effector design.

  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphofructokinase, muscle type
A, B
762Oryctolagus cuniculusMutation(s): 0 
Gene Names: PFKM
Find proteins for P00511 (Oryctolagus cuniculus)
Explore P00511 
Go to UniProtKB:  P00511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00511
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A],
I [auth B],
K [auth B]
C10 H16 N5 O13 P3
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
C10 H15 N5 O10 P2
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
L [auth B]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.684α = 90
b = 163.684β = 90
c = 356.582γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description