5I5A

quasi racemic structure of allo-Ile7-ShK and D-ShK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin.

Dang, B.Shen, R.Kubota, T.Mandal, K.Bezanilla, F.Roux, B.Kent, S.B.

(2017) Angew. Chem. Int. Ed. Engl. 56: 3324-3328

  • DOI: 10.1002/anie.201612398
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ShK toxin is a cysteine-rich 35-residue protein ion-channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the proper ...

    ShK toxin is a cysteine-rich 35-residue protein ion-channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the properties of the ShK protein. Molecular dynamics simulations were used to calculate the free energy cost of inverting the side-chain stereochemistry of individual Thr or Ile residues. Guided by the computational results, we used chemical protein synthesis to prepare three ShK polypeptide chain analogues, each containing either an allo-Thr or an allo-Ile residue. The three allo-Thr or allo-Ile-containing ShK polypeptides were able to fold into defined protein products, but with different folding propensities. Their relative thermal stabilities were measured and were consistent with the MD simulation data. Structures of the three ShK analogue proteins were determined by quasi-racemic X-ray crystallography and were similar to wild-type ShK. All three ShK analogues retained ion-channel blocking activity.


    Organizational Affiliation

    Department of Chemistry, Department of Biochemistry & Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kappa-stichotoxin-She3a
A
35Stichodactyla helianthusMutation(s): 0 
Find proteins for P29187 (Stichodactyla helianthus)
Go to UniProtKB:  P29187
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-ShK
B
35N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

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Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
MLT
Query on MLT

Download SDF File 
Download CCD File 
B
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
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  15 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DCY
Query on DCY
B
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DPR
Query on DPR
B
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DHI
Query on DHI
B
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
B
D-PEPTIDE LINKINGC3 H7 N O3

--

DTH
Query on DTH
B
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

DPN
Query on DPN
B
D-PEPTIDE LINKINGC9 H11 N O2

--

DGN
Query on DGN
B
D-PEPTIDE LINKINGC5 H10 N2 O3

--

MED
Query on MED
B
D-PEPTIDE LINKINGC5 H11 N O2 S

--

DAS
Query on DAS
B
D-PEPTIDE LINKINGC4 H7 N O4

--

DTY
Query on DTY
B
D-PEPTIDE LINKINGC9 H11 N O3

--

DAR
Query on DAR
B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.849α = 90.00
b = 17.656β = 101.61
c = 49.469γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references
  • Version 1.2: 2017-03-29
    Type: Database references