4OEE

Crystal Structure Analysis of FGF2-Disaccharide (S3I2) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interactions that influence the binding of synthetic heparan sulfate based disaccharides to fibroblast growth factor-2.

Li, Y.C.Ho, I.H.Ku, C.C.Zhong, Y.Q.Hu, Y.P.Chen, Z.G.Chen, C.Y.Lin, W.C.Zulueta, M.M.Hung, S.C.Lin, M.G.Wang, C.C.Hsiao, C.D.

(2014) Acs Chem.Biol. 9: 1712-1717

  • DOI: 10.1021/cb500298q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heparan sulfate (HS) is a linear sulfated polysaccharide that mediates protein activities at the cell-extracellular interface. Its interactions with proteins depend on the complex patterns of sulfonations and sugar residues. Previously, we synthesize ...

    Heparan sulfate (HS) is a linear sulfated polysaccharide that mediates protein activities at the cell-extracellular interface. Its interactions with proteins depend on the complex patterns of sulfonations and sugar residues. Previously, we synthesized all 48 potential disaccharides found in HS and used them for affinity screening and X-ray structural analysis with fibroblast growth factor-1 (FGF1). Herein, we evaluated the affinities of the same sugars against FGF2 and determined the crystal structures of FGF2 in complex with three disaccharides carrying N-sulfonated glucosamine and 2-O-sulfonated iduronic acid as basic backbones. The crystal structures show that water molecules mediate different interactions between the 3-O-sulfonate group and Lys125. Moreover, the 6-O-sulfonate group forms intermolecular interactions with another FGF2 unit apart from the main binding site. These findings suggest that the water-mediated interactions and the intermolecular interactions influence the binding affinity of different disaccharides with FGF2, correlating with their respective dissociation constants in solution.


    Organizational Affiliation

    Institute of Molecular Biology, ‡Genomics Research Center, and §Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibroblast growth factor 2
A
155Homo sapiensMutation(s): 2 
Gene Names: FGF2 (FGFB)
Find proteins for P09038 (Homo sapiens)
Go to Gene View: FGF2
Go to UniProtKB:  P09038
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IDY
Query on IDY

Download SDF File 
Download CCD File 
A
methyl 2-O-sulfo-alpha-L-idopyranosiduronic acid
C7 H12 O10 S
OBWAEUUFHKKIQN-QVVHOTIMSA-N
 Ligand Interaction
GNX
Query on GNX

Download SDF File 
Download CCD File 
A
2-deoxy-3-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
C6 H13 N O11 S2
AJBMJMMLWNUEAC-UKFBFLRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.441α = 90.00
b = 58.136β = 109.10
c = 32.395γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-13 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Li, Y.C., Hsiao, C.D.

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2018-04-04
    Type: Data collection