5N8T

CRYSTAL STRUCTURE OF STREPTAVIDIN D-amino acid containing peptide Gdlwqheatwkkq


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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:  
    5N7X, 5N89, 5N99, 5N8W, 5N8T, 5N8J, 5N8B, 5N8E

  • 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 screening and stepwise evolution, to discover novel peptide hotspots ...

    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. jigar.patel@roche.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
StreptavidinA183Streptomyces avidiniiMutation(s): 0 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTR (Subject of Investigation/LOI)
Query on DTR

Download Ideal Coordinates CCD File 
C [auth A], I [auth A]D-TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-SECBINFHSA-N
 Ligand Interaction
DHI (Subject of Investigation/LOI)
Query on DHI

Download Ideal Coordinates CCD File 
E [auth A]D-HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-RXMQYKEDSA-O
 Ligand Interaction
DGL
Query on DGL

Download Ideal Coordinates CCD File 
F [auth A]D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
DLY
Query on DLY

Download Ideal Coordinates CCD File 
J [auth A]D-LYSINE
C6 H14 N2 O2
KDXKERNSBIXSRK-RXMQYKEDSA-N
 Ligand Interaction
DGN
Query on DGN

Download Ideal Coordinates CCD File 
D [auth A]D-GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-GSVOUGTGSA-N
 Ligand Interaction
DLE
Query on DLE

Download Ideal Coordinates CCD File 
B [auth A]D-LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-RXMQYKEDSA-N
 Ligand Interaction
DTH
Query on DTH

Download Ideal Coordinates CCD File 
H [auth A]D-THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-STHAYSLISA-N
 Ligand Interaction
DAL
Query on DAL

Download Ideal Coordinates CCD File 
G [auth A]D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.779α = 90
b = 57.779β = 90
c = 84.405γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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