2BHK

Crystal structure of human growth and differentiation factor 5 (GDF5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

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This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of Recombinant Human Growth Differentiation Factor 5. Evidence for Interaction of the Type I and Type II Receptor Binding Sites.

Schreuder, H.Liesum, A.Pohl, J.Kruse, M.Koyama, M.

(2005) Biochem Biophys Res Commun 329: 1076

  • DOI: https://doi.org/10.1016/j.bbrc.2005.02.078
  • Primary Citation of Related Structures:  
    2BHK

  • PubMed Abstract: 

    The crystal structure of human growth differentiation factor 5 (GDF5) was solved at 2.4A resolution. The structure is very similar to the structure of bone morphogenetic factor 7 (BMP7) and consists of two banana-shaped monomers, linked via a disulfide bridge. The crystal packing of GDF5 is the same as the crystal packing of BMP7. This is highly unusual since only 25-30% of the crystal contacts involve identical residues. Analysis of the crystal packing revealed that residues of the type I receptor epitope are binding to residues of the type II receptor-binding epitope. The fact that for both BMP family members the type I and type II receptor-binding sites interact suggests that the complementary sites on the receptors may interact as well, suggesting a way how preformed receptor heterodimers may form, similar to the preformed receptors observed for the erythropoietin receptor and the BMP2 receptors.


  • Organizational Affiliation

    sanofi-aventis, Industriepark Hoechst, Building G 865, A-65926 Frankfurt, Germany. Herman.Schreuder@sanofi-aventis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GROWTH DIFFERENTIATION FACTOR 5120Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43026 (Homo sapiens)
Explore P43026 
Go to UniProtKB:  P43026
PHAROS:  P43026
GTEx:  ENSG00000125965 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43026
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.2α = 90
b = 98.2β = 90
c = 43.7γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description