3F9M

Human pancreatic glucokinase in complex with glucose and activator showing a mobile flap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The active conformation of human glucokinase is not altered by allosteric activators

Petit, P.Antoine, M.Ferry, G.Boutin, J.A.Lagarde, A.Gluais, L.Vincentelli, R.Vuillard, L.

(2011) Acta Crystallogr D Biol Crystallogr 67: 929-935

  • DOI: 10.1107/S0907444911036729
  • Primary Citation of Related Structures:  
    3F9M, 3FGU, 3ID8, 3IDH, 4NO7

  • PubMed Abstract: 
  • Glucokinase (GK) catalyses the formation of glucose 6-phosphate from glucose and ATP. A specific feature of GK amongst hexokinases is that it can cycle between active and inactive conformations as a function of glucose concentration, resulting in a unique positive kinetic cooperativity with glucose, which turns GK into a unique key sensor of glucose metabolism, notably in the pancreas ...

    Glucokinase (GK) catalyses the formation of glucose 6-phosphate from glucose and ATP. A specific feature of GK amongst hexokinases is that it can cycle between active and inactive conformations as a function of glucose concentration, resulting in a unique positive kinetic cooperativity with glucose, which turns GK into a unique key sensor of glucose metabolism, notably in the pancreas. GK is a target of antidiabetic drugs aimed at the activation of GK activity, leading to insulin secretion. Here, the first structures of a GK-glucose complex without activator, of GK-glucose-AMP-PNP and of GK-glucose-AMP-PNP with a bound activator are reported. All these structures are extremely similar, thus demonstrating that binding of GK activators does not result in conformational changes of the active protein but in stabilization of the active form of GK.


    Organizational Affiliation

    BioXtal, PX Unit, c/o AFMB, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlucokinaseA470Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35557 (Homo sapiens)
Explore P35557 
Go to UniProtKB:  P35557
PHAROS:  P35557
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRK (Subject of Investigation/LOI)
Query on MRK

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-4-FLUORO-5-[(1-METHYL-1H-IMIDAZOL-2-YL)SULFANYL]-N-(1,3-THIAZOL-2-YL)BENZAMIDE
C14 H12 F N5 O S2
YUCYMQBDBXVNCE-UHFFFAOYSA-N
 Ligand Interaction
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
B [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MRK BindingDB:  3F9M Kd: 360 (nM) from 1 assay(s)
EC50: 67.11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.7α = 90
b = 81.2β = 90
c = 85.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-09
    Changes: Database references
  • Version 1.3: 2012-04-25
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary