4KVU

Crystal structure of a 6-helix coiled coil CC-Hex-L17C-W224BF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Accessibility, Reactivity, and Selectivity of Side Chains within a Channel of de Novo Peptide Assembly.

Burton, A.J.Thomas, F.Agnew, C.Hudson, K.L.Halford, S.E.Brady, R.L.Woolfson, D.N.

(2013) J.Am.Chem.Soc. 135: 12524-12527

  • DOI: 10.1021/ja4053027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ab initio design of enzymes requires precise and predictable positioning of reactive functional groups within accessible and controlled environments of de novo protein scaffolds. Here we show that multiple thiol moieties can be placed within a centra ...

    Ab initio design of enzymes requires precise and predictable positioning of reactive functional groups within accessible and controlled environments of de novo protein scaffolds. Here we show that multiple thiol moieties can be placed within a central channel, with approximate dimensions 6 × 42 Å, of a de novo, six-helix peptide assembly (CC-Hex). Layers of six cysteine residues are introduced at two different sites ~6 (the "L24C" mutant) and ~17 Å (L17C) from the C-terminal opening of the channel. X-ray crystal structures confirm the mutant structures as hexamers with internal free thiol, rather than disulfide-linked cysteine residues. Both mutants are hexa-alkylated upon addition of iodoacetamide, demonstrating accessibility and full reactivity of the thiol groups. Comparison of the alkylation and unfolding rates of the hexamers indicates that access is directly through the channel and not via dissociation and unfolding of the assembly. Moreover, neither mutant reacts with iodoacetic acid, demonstrating selectivity of the largely hydrophobic channel. These studies show that it is possible to engineer reactive side chains with both precision and control into a de novo scaffold to produce protein-like structures with chemoselective reactivity.


    Organizational Affiliation

    School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-helix coiled coil CC-Hex-L17C-W224BF
A, B, C
33N/AMutation(s): 0 
N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
4BF
Query on 4BF
A, B, C
L-PEPTIDE LINKINGC9 H10 Br N O2TYR
ACE
Query on ACE
A, B, C
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 57.010α = 90.00
b = 60.980β = 90.00
c = 125.440γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
DNAdata collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references