1FC0

HUMAN LIVER GLYCOGEN PHOSPHORYLASE COMPLEXED WITH N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core.

Rath, V.L.Ammirati, M.LeMotte, P.K.Fennell, K.F.Mansour, M.N.Danley, D.E.Hynes, T.R.Schulte, G.K.Wasilko, D.J.Pandit, J.

(2000) Mol Cell 6: 139-148

  • Primary Citation of Related Structures:  
    1FA9, 1FC0

  • PubMed Abstract: 
  • Glycogen phosphorylases catalyze the breakdown of glycogen to glucose-1-phosphate, which enters glycolysis to fulfill the energetic requirements of the organism. Maintaining control of blood glucose levels is critical in minimizing the debilitating effects of diabetes, making liver glycogen phosphorylase a potential therapeutic target ...

    Glycogen phosphorylases catalyze the breakdown of glycogen to glucose-1-phosphate, which enters glycolysis to fulfill the energetic requirements of the organism. Maintaining control of blood glucose levels is critical in minimizing the debilitating effects of diabetes, making liver glycogen phosphorylase a potential therapeutic target. To support inhibitor design, we determined the crystal structures of the active and inactive forms of human liver glycogen phosphorylase a. During activation, forty residues of the catalytic site undergo order/disorder transitions, changes in secondary structure, or packing to reorganize the catalytic site for substrate binding and catalysis. Knowing the inactive and active conformations of the liver enzyme and how each differs from its counterpart in muscle phosphorylase provides the basis for designing inhibitors that bind preferentially to the inactive conformation of the liver isozyme.


    Organizational Affiliation

    Exploratory Medicinal Sciences, Global Research and Development, Groton Laboratories, Pfizer, Inc, Connecticut 06340, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOGEN PHOSPHORYLASE, LIVER FORMA, B846Homo sapiensMutation(s): 0 
Gene Names: PYGL
EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens)
Explore P06737 
Go to UniProtKB:  P06737
PHAROS:  P06737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06737
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
NBG
Query on NBG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
N-acetyl-beta-D-glucopyranosylamine
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124α = 90
b = 124β = 90
c = 122.28γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary