6IMG | pdb_00006img

Solution Structure of Bicyclic Peptide pb-13


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Ordered and Isomerically Stable Bicyclic Peptide Scaffolds Constrained through Cystine Bridges and Proline Turns.

Lin, P.Yao, H.Zha, J.Zhao, Y.Wu, C.

(2019) Chembiochem 20: 1514-1518

  • DOI: https://doi.org/10.1002/cbic.201800788
  • Primary Citation Related Structures: 
    6IMG, 6IMH

  • PubMed Abstract: 

    Bicyclic peptides are attractive scaffolds for the design of potent protein binders and new therapeutics. However, peptide bicycles constrained through disulfide bonds are rarely stable or tolerant to sequence manipulation owing to disulfide isomerization, especially for peptides lacking a regular secondary structure. Herein, we report the discovery and identification of a class of bicyclic peptide scaffolds with ordered but irregular secondary structures. These peptides have a conserved cysteine/proline framework for directing the oxidative folding into a fused bicyclic structure that consists of four irregular turns and a 3 10 helix (characterized by NMR spectroscopy). This work shows that bicyclic peptides can be stabilized into ordered structures by manipulating both the disulfide bonds and proline-stabilized turns. In turn, this could inspire the design and engineering of multicyclic peptides with new structures and benefit the development of novel protein binders and therapeutics.


  • Organizational Affiliation
    • Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, Xiamen University, Xiamen, 361005, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 1.89 kDa 
  • Atom Count: 131 
  • Modeled Residue Count: 18 
  • Deposited Residue Count: 18 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
(ACE)-GLY-CYS-PRO-CYS-ILE-TRP-PRO-GLU-LEU-CYS-PRO-TRP-ILE-ARG-SER-CYS-(NH2)18Inovirus M13Mutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary