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Biology LibreTexts

iCn3D Tutorial: Protein Kinase B (AKT)

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Protein Kinase B (AKT)

A more complicated protein with multiple domains and at least two major conformations with different PDB structures: Protein Kinase B (aka AKT)

PDB files:

  • 3CQW (active)
  • 3O96  (inactive)
  • 1UNQ  PH domain

A.  Exploration of AKT – Domain Structure

  • PDB ID: 1UNQ
  • Description: Pleckstrin Homology Domain Of Protein Kinase B/Akt Bound To Ins(1,3,4,5)-Tetrakisphophate
  1. Open new iCn3D
  2. File, Retrieve by ID, MMDB
  3. Alt Click the ligand.  Style, Chemicals, Sphere
  4. Select, Select on 3D, check Chain, alt click the protein
  5. Color,  Secondary, Sheets in Yellow

With the protein still selected:

  1. Analysis, Interactions
  2. For the second set choose chemicals
  3. Check just the noncovalent interactions shown below

    clipboard_e86b03ae938dbc70e2c3e0fc82f4120de.png
     
  4. Choose 3D Display Interactions.  This will display interacting side chains
  5. Selections, Save Selections, name it Interactions
  6. Style, Sidechains, Stick (so next step will just color side chains)
  7. Color, atom
  8. In defined sets choose Interactions.  Analysis, Label, Per Residue & No.
  9. Analysis, Label Scale, 3
  10. Style, Background, White
  11. File, Share Link, copy short link

B.  Exploration of AKT – Self-defined aa, sequences, Render PH-domain, N-lobe, C-Lobe, Catalytic Loop, Activation Loop

PDB ID: 3O96 (inactive)

Description

  • Crystal Structure of Human AKT1 with an Allosteric Inhibitor
  • RAC-alpha serine/threonine-protein kinase; Chain A
  • Allosteric inhibitor IQO

Cartoon structure

clipboard_ed0412281c36fa1a7152b6d9d3529a4fa.png

Instructions

  1. File, Retrieve by ID, MMDB
  2. Analysis, Seq. & Annotations, Uncheck Conserved Domains
  3. Analysis, Defined Sets.  Click 1st domain (PH = top 3O96_A_3d_domain)
  4. Style, Protein, C-Alpha Trace.
  5. Color , Unicolor, Yellow
  6. Defined Sets.  Choose 2st domain (N-Lobe).  Color, unicolor, Cyan
  7. Defined Sets.  Choose 3st domain (C-Lobe).  Color, unicolor, Grey, Light Gray
  8. Seq. & Annotations, Details  Tab, Uncheck Conserved Domains.
  9. Select by hand the catalytic  loop  (table below) by using the horizontal scroll to find and select 271V-287H.  Hover over each amino acids and click to select it or use your mouse to sweep out a rectangle over all the range of amino acids.
  10. Select, Save Selection, CatLoop
  11. Color, Unicolor, Red
  12. Repeat for Activation Loop and save the selection. Color Unicolor, Blue
  13. Style, Background, White
  14. File, Share Link, Lifelong Short Link

Numbering or generic kinase and AKT

SITE

Generic
Kinase

Akt (+108)

N lobe

K72

K180

N lobe

E91

E199

C lobe, cat loop

R165

R273

C lobe, cat loop

D166

D274

C lobe, act loop

D184

D292

C lobe, act loop

 

T197

T305
(NO SEQ)

Approx Cat Loop

163-179

271V—287H

 

Approx Act loop

Start DFG (292-294) to APE

184-200

292-319

308Tmiss toAPE end 319

 

C.  Compare 3CQW (active) and 3O96  (inactive) – Superimpose two AKT structures

PDB ID: 3CQW and 3O96

Description

3O96 (inactive): Crystal Structure of Human AKT1 with an Allosteric Inhibitor

  • RAC-alpha serine/threonine-protein kinase; Chain A
  • Allosteric inhibitor IQO

3CQW (active):

  • Crystal Structure of Akt-1 complexed with substrate peptide (hence active form) and inhibitor
  • Peptide:  Glycogen synthase kinase-3 beta peptide

Instructions

  1. File, Align, Structure to Structure
  2. Input 3CQW and 3O96
  3. Choose All Matching Molecules Superimposed
  4. In the top of the right hand alignment window, save the aligned state as presented (al_seq1).  Just the aligned sequences will be highlighted.
  5. View,  View Selection
  6. Style, Background, White
  7. File, Share Link, Lifelong Short Link
  8. Toggle between the two states by clicking the toggle menu button just underneath the File menu button

iCn3D Tutorial: Protein Kinase B (AKT) is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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