2BHK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.bbrc.2005.02.078

  • 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 disulfi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GROWTH DIFFERENTIATION FACTOR 5
A
120Homo sapiensMutation(s): 0 
Gene Names: GDF5 (BMP14, CDMP1)
Find proteins for P43026 (Homo sapiens)
Go to Gene View: GDF5
Go to UniProtKB:  P43026
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.200α = 90.00
b = 98.200β = 90.00
c = 43.700γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection