Crystal structure of glucokinase regulatory protein complexed to fructose-1-phosphate

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Crystal Structure of Glucokinase Regulatory Protein.

Pautsch, A.Stadler, N.Loehle, A.Rist, W.Berg, A.Glocker, L.Nar, H.Reinert, D.Lenter, M.Heckel, A.Schnapp, G.Kauschke, S.G.

(2013) Biochemistry 52: 3523

  • DOI: https://doi.org/10.1021/bi4000782
  • Primary Citation of Related Structures:  
    4BB9, 4BBA

  • PubMed Abstract: 

    Glucokinase (GK) plays a major role in the regulation of blood glucose homeostasis in both the liver and the pancreas. In the liver, GK is controlled by the GK regulatory protein (GKRP). GKRP in turn is activated by fructose 6-phosphate (F6P) and inactivated by fructose 1-phosphate (F1P). Disrupting the GK-GKRP complex increases the activity of GK in the cytosol and is considered an attractive concept for the regulation of blood glucose. We have determined the crystal structure of GKRP in its inactive F1P-bound form. The binding site for F1P is located deeply buried at a domain interface, and H-D exchange experiments confirmed that F1P and F6P compete for this site. The structure of the inactive GKRP-F1P complex provides a starting point for understanding the mechanism of fructose phosphate-dependent GK regulation at an atomic level.

  • Organizational Affiliation

    Departments of Lead Identification and Optimization Support, ‡CardioMetabolic Diseases Research, §CNS Diseases Research, ∥Drug Discovery Support, ⊥BP Process Science, and @Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Company KG , Biberach an der Riss, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUCOKINASE REGULATORY PROTEIN633Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14397 (Homo sapiens)
Explore Q14397 
Go to UniProtKB:  Q14397
PHAROS:  Q14397
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14397
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on F1P

Download Ideal Coordinates CCD File 
B [auth A]1-O-phosphono-beta-D-fructopyranose
C6 H13 O9 P
Query on CA

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
F1P PDBBind:  4BB9 Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.97α = 90
b = 72.3β = 90
c = 136.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata 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: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Structure summary