5N99

CRYSTAL STRUCTURE OF STREPTAVIDIN with cyclic peptide NQpWQ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target.

Lyamichev, V.I.Goodrich, L.E.Sullivan, E.H.Bannen, R.M.Benz, J.Albert, T.J.Patel, J.J.

(2017) Sci Rep 7: 12116-12116

  • DOI: 10.1038/s41598-017-12440-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Considerable efforts have been made to develop technologies for selection of peptidic molecules that act as substrates or binders to a protein of interest. Here we demonstrate the combination of rational peptide array library design, parallel screeni ...

    Considerable efforts have been made to develop technologies for selection of peptidic molecules that act as substrates or binders to a protein of interest. Here we demonstrate the combination of rational peptide array library design, parallel screening and stepwise evolution, to discover novel peptide hotspots. These hotspots can be systematically evolved to create high-affinity, high-specificity binding peptides to a protein target in a reproducible and digitally controlled process. The method can be applied to synthesize both linear and cyclic peptides, as well as peptides composed of natural and non-natural amino acid analogs, thereby enabling screens in a much diverse chemical space. We apply this method to stepwise evolve peptide binders to streptavidin, a protein studied for over two decades and report novel peptides that mimic key interactions of biotin to streptavidin.


    Organizational Affiliation

    Roche Madison, 500 S Rosa Rd, Madison, WI, 53719, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B, D, G, I, K, M, O, Q, S, U, Y
183Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ASN-GLN-DPR-TRP-GLN
C, E, F, H, J, L, N, P, R, T, V, X
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DPR
Query on DPR
C, E, F, H, J, L, N, P, R, T, V, X
D-PEPTIDE LINKINGC5 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.744α = 90.00
b = 115.315β = 90.00
c = 210.369γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
XDSdata reduction
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release