Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 13.90 kDa 
• Atom Count: 926 
• Modelled Residue Count: 105 
• Deposited Residue Count: 120 
• Unique protein chains: 1

2BHK

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

• PDB DOI: 10.2210/pdb2BHK/pdb

• Classification: GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-12 Released: 2005-03-11 
• Deposition Author(s): Schreuder, H., Liesum, A., Pohl, J., Kruse, M., Koyama, M.

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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 

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

• PubMed: 15752764 
• DOI: 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.

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Organizational Affiliation: 

sanofi-aventis, Industriepark Hoechst, Building G 865, A-65926 Frankfurt, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GROWTH DIFFERENTIATION FACTOR 5	A	120	Homo sapiens	Mutation(s): 0  Gene Names: GDF5, BMP14, CDMP1
UniProt & NIH Common Fund Data Resources
Find proteins for P43026 (Homo sapiens) Explore P43026  Go to UniProtKB:  P43026
PHAROS:  P43026 GTEx:  ENSG00000125965

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

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 = 98.2	α = 90
b = 98.2	β = 90
c = 43.7	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-12 
• Released Date: 2005-03-11 
Deposition Author(s): Schreuder, H., Liesum, A., Pohl, J., Kruse, M., Koyama, M.

Revision History  

• 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