4GLS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.USA 109: 14779-14784

  • DOI: 10.1073/pnas.1210483109
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D- Vascular endothelial growth factor-A
A, B
102N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L- RFX001
C, G
56N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
D- RFX001
D, H
56N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor A
E, F
102Homo sapiensMutation(s): 0 
Gene Names: VEGFA (VEGF)
Find proteins for P15692 (Homo sapiens)
Go to Gene View: VEGFA
Go to UniProtKB:  P15692
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  19 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
A, B, D, H
D-PEPTIDE LINKINGC6 H13 N O2

--

DCY
Query on DCY
A, B
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DPR
Query on DPR
A, B
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
A, B, D, H
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DHI
Query on DHI
A, B
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
A, B, D, H
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
A, B, D, H
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
A, B, D, H
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
A, B, D, H
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
A, B, D, H
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
D, H
D-PEPTIDE LINKINGC3 H7 N O2

--

DPN
Query on DPN
A, B, D, H
D-PEPTIDE LINKINGC9 H11 N O2

--

DGN
Query on DGN
A, B
D-PEPTIDE LINKINGC5 H10 N2 O3

--

MED
Query on MED
A, B
D-PEPTIDE LINKINGC5 H11 N O2 S

--

DAS
Query on DAS
A, B, D, H
D-PEPTIDE LINKINGC4 H7 N O4

--

DSG
Query on DSG
A, B, D, H
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DTR
Query on DTR
D, H
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DTY
Query on DTY
A, B, D, H
D-PEPTIDE LINKINGC9 H11 N O3

--

DAR
Query on DAR
A, B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.156α = 90.00
b = 88.322β = 99.98
c = 77.866γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2013-05-29
    Type: Structure summary
  • Version 1.2: 2013-11-27
    Type: Database references