3O8N | pdb_00003o8n

Structure of phosphofructokinase from rabbit skeletal muscle

PDB DOI: https://doi.org/10.2210/pdb3O8N/pdb

Classification: TRANSFERASE
Organism(s): Oryctolagus cuniculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-03 Released: 2011-02-02
Deposition Author(s): Banaszak, K., Chang, S.H., Rypniewski, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.302 (Depositor), 0.298 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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 Biology 407: 284-297

PubMed: 21241708 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2011.01.019
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 169.67 kDa
Atom Count: 11,630
Modeled Residue Count: 1,496
Deposited Residue Count: 1,524
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructokinase, muscle type	A, B	762	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: PFKM EC: 2.7.1.11
UniProt
Find proteins for P00511 (Oryctolagus cuniculus) Explore P00511 Go to UniProtKB: P00511
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00511
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.302 (Depositor), 0.298 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.292	α = 90
b = 163.292	β = 90
c = 356.939	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

Banaszak, K.

Chang, S.H.

Rypniewski, W.

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