Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21/n

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.

Mandal, K.Uppalapati, M.Ault-Riche, D.Kenney, J.Lowitz, J.Sidhu, S.S.Kent, S.B.

(2012) Proc Natl Acad Sci U S A 109: 14779-14784

  • DOI: https://doi.org/10.1073/pnas.1210483109
  • Primary Citation of Related Structures:  
    4GLN, 4GLS, 4GLU

  • PubMed Abstract: 

    Total chemical synthesis was used to prepare the mirror image (D-protein) form of the angiogenic protein vascular endothelial growth factor (VEGF-A). Phage display against D-VEGF-A was used to screen designed libraries based on a unique small protein scaffold in order to identify a high affinity ligand. Chemically synthesized D- and L- forms of the protein ligand showed reciprocal chiral specificity in surface plasmon resonance binding experiments: The L-protein ligand bound only to D-VEGF-A, whereas the D-protein ligand bound only to L-VEGF-A. The D-protein ligand, but not the L-protein ligand, inhibited the binding of natural VEGF(165) to the VEGFR1 receptor. Racemic protein crystallography was used to determine the high resolution X-ray structure of the heterochiral complex consisting of {D-protein antagonist + L-protein form of VEGF-A}. Crystallization of a racemic mixture of these synthetic proteins in appropriate stoichiometry gave a racemic protein complex of more than 73 kDa containing six synthetic protein molecules. The structure of the complex was determined to a resolution of 1.6 Å. Detailed analysis of the interaction between the D-protein antagonist and the VEGF-A protein molecule showed that the binding interface comprised a contact surface area of approximately 800 Å(2) in accord with our design objectives, and that the D-protein antagonist binds to the same region of VEGF-A that interacts with VEGFR1-domain 2.

  • Organizational Affiliation

    Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-RFX001A [auth D],
D [auth H]
56synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor AB [auth E],
C [auth F]
102Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens)
Explore P15692 
Go to UniProtKB:  P15692
PHAROS:  P15692
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15692
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21/n 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.156α = 90
b = 88.322β = 99.98
c = 77.866γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Structure summary
  • Version 1.2: 2013-11-27
    Changes: Database references
  • Version 1.3: 2019-04-10
    Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-04-24
    Changes: Data collection, Refinement description