4WPB

Vascular endothelial growth factor in complex with alpha/beta-VEGF-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Targeting diverse protein-protein interaction interfaces with alpha / beta-peptides derived from the Z-domain scaffold.

Checco, J.W.Kreitler, D.F.Thomas, N.C.Belair, D.G.Rettko, N.J.Murphy, W.L.Forest, K.T.Gellman, S.H.

(2015) Proc Natl Acad Sci U S A 112: 4552-4557

  • DOI: https://doi.org/10.1073/pnas.1420380112
  • Primary Citation of Related Structures:  
    4WPB

  • PubMed Abstract: 

    Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both α- and β-amino acid residues ("α/β-peptides") that mimic several peptides derived from the three-helix bundle "Z-domain" scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain-mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications.


  • Organizational Affiliation

    Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor A
A, B
102Homo sapiensMutation(s): 0 
Gene Names: VEGFAVEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens)
Explore P15692 
Go to UniProtKB:  P15692
PHAROS:  P15692
GTEx:  ENSG00000112715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15692
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
alpha/beta-VEGF-1
C, D
40Staphylococcus aureusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
C, D
L-PEPTIDE LINKINGC4 H9 N O2ALA
B3D
Query on B3D
C, D
L-PEPTIDE LINKINGC5 H9 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.1α = 90
b = 78.4β = 102.8
c = 56.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM056414
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008349

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-07-10
    Changes: Data collection