Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

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The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding.

Gregoriou, M.Noble, M.E.Watson, K.A.Garman, E.F.Krulle, T.M.de la Fuente, C.Fleet, G.W.Oikonomakos, N.G.Johnson, L.N.

(1998) Protein Sci 7: 915-927

  • DOI: https://doi.org/10.1002/pro.5560070409
  • Primary Citation of Related Structures:  
    1A8I, 2GPN

  • PubMed Abstract: 

    A glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that contribute to the binding, the structures of GPb in the native T state conformation and in complex with glucopyranose spirohydantoin have been determined at 100 K to 2.0 A and 1.8 A resolution, respectively, and refined to crystallographic R values of 0.197 (R[free] 0.248) and 0.182 (R[free] 0.229), respectively. The low temperature structure of GPb is almost identical to that of the previously determined room temperature structure, apart from a decrease in overall atomic temperature factors ((B) room temperature GPb = 34.9 A2; (B) 100 K GPb = 23.4 A2). The glucopyranose spirohydantoin inhibitor (Ki = 3.0 microM) binds at the catalytic site and induces small changes in two key regions of the protein: the 280s loop (residues 281-286) that results in a decrease in mobility of this region, and the 380s loop (residues 377-385) that undergoes more significant shifts in order to optimize contact to the ligand. The hydantoin group, that is responsible for increasing the affinity of the glucose compound by a factor of 10(3), makes only one hydrogen bond to the protein, from one of its NH groups to the main chain oxygen of His377. The other polar groups of the hydantoin group form hydrogen bonds to five water molecules. These waters are involved in extensive networks of hydrogen bonds and appear to be an integral part of the protein structure. Analysis of the water structure at the catalytic site of the native enzyme, shows that five waters are displaced by ligand binding and that there is a significant decrease in mobility of the remaining waters on formation of the GPb-hydantoin complex. The ability of the inhibitor to exploit existing waters, to displace waters and to recruit new waters appears to be important for the high affinity of the inhibitor.

  • Organizational Affiliation

    Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, University of Oxford, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOGEN PHOSPHORYLASE B842Oryctolagus cuniculusMutation(s): 1 
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLS

Download Ideal Coordinates CCD File 
C8 H12 N2 O7
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
Binding Affinity Annotations 
IDSourceBinding Affinity
GLS PDBBind:  1A8I Ki: 3000 (nM) from 1 assay(s)
Binding MOAD:  1A8I Ki: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.47α = 90
b = 127.47β = 90
c = 115.8γ = 90
Software Package:
Software NamePurpose
CCP4model building
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: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2023-08-02
    Changes: Database references, Refinement description