De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1073/pnas.1710695114
  • Primary Citation of Related Structures:  
    5V2G, 5V2O, 5WOC, 5WOD

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
60synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2PE

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
O [auth C],
S [auth D]
C18 H38 O10
Query on TMM

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
P [auth C]
T [auth D]
W [auth E]
I [auth A],
L [auth B],
P [auth C],
T [auth D],
W [auth E],
Z [auth F]
C9 H6 O6
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
Q [auth D]
U [auth E]
G [auth A],
J [auth B],
M [auth C],
Q [auth D],
U [auth E],
X [auth F],
Y [auth F]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
N [auth C],
R [auth D],
V [auth E]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.77α = 89.79
b = 55.34β = 108.15
c = 58.04γ = 109.52
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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