9GPB

THE ALLOSTERIC TRANSITION OF GLYCOGEN PHOSPHORYLASE

• PDB DOI: https://doi.org/10.2210/pdb9GPB/pdb

• Classification: GLYCOGEN PHOSPHORYLASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 1990-12-17 Released: 1992-10-15 
• Deposition Author(s): Barford, D., Johnson, L.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 
  0.177 (Depositor) 

Literature

The allosteric transition of glycogen phosphorylase.

Barford, D., Johnson, L.N.

(1989) Nature 340: 609-616

• PubMed: 2770867 
• DOI: https://doi.org/10.1038/340609a0
• Primary Citation of Related Structures:  
  9GPB


• PubMed Abstract: 
  

  The crystal structure of R-state glycogen phosphorylase b has been determined at 2.9 A resolution. A comparison of T-state and R-state structures of the enzyme explains its cooperative behaviour on ligand binding and the allosteric regulation of its activity. Communication between catalytic sites of the dimer is provided by a change in packing geometry of two helices linking each site with the subunit interface. Activation by AMP or by phosphorylation results in a quaternary conformational change that switches these two helices into the R-state conformation.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, University of Oxford, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 391.23 kDa 
• Atom Count: 26,873 
• Modelled Residue Count: 3,292 
• Deposited Residue Count: 3,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A, B, C, D	842	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: PYGM EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work:  0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119	α = 90
b = 190	β = 109.35
c = 88.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-10-15 
Deposition Author(s): Barford, D., Johnson, L.N.

Revision History  

• Version 1.0: 1992-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary