5WOC

De Novo Design of Covalently Constrained Meso-size Protein Scaffolds with Unique Tertiary Structures


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


This is version 1.2 of the entry. See complete history


Literature

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures.

Dang, B.Wu, H.Mulligan, V.K.Mravic, M.Wu, Y.Lemmin, T.Ford, A.Silva, D.A.Baker, D.DeGrado, W.F.

(2017) Proc Natl Acad Sci U S A 114: 10852-10857

  • DOI: 10.1073/pnas.1710695114
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approac ...

    The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature. Here we use Rosetta and Tertiary Motifs (TERMs) to design small proteins that fold around multivalent cross-linkers. The hydrophobic cross-linkers stabilize the fold by macrocyclic restraints, and they also form an integral part of a small apolar core. The designed CovCore proteins were prepared by chemical synthesis, and their structures were determined by solution NMR or X-ray crystallography. These mesosized proteins, lying between conventional proteins and small peptides, are easily accessible either through biosynthetic precursors or chemical synthesis. The unique tertiary structures and ease of synthesis of CovCore proteins indicate that they should provide versatile templates for developing inhibitors of protein-protein interactions.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; william.degrado@ucsf.edu.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SER-PRO-GLU-GLU-ARG-ALA-GLN-LEU-CYS-THR-ALA-ALA-GLU-LYS-ALA-ASP-GLU-LEU-GLY
A, B
19synthetic constructMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B74
Query on B74

Download CCD File 
A
(3-methylphenyl)methanol
C8 H10 O
JJCKHVUTVOPLBV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 5WOC Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Database references