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
- Open new iCn3D
- File, Retrieve by ID, MMDB
- Alt Click the ligand. Style, Chemicals, Sphere
- Select, Select on 3D, check Chain, alt click the protein
- Color, Secondary, Sheets in Yellow
With the protein still selected:
- Analysis, Interactions
- For the second set choose chemicals
- Check just the noncovalent interactions shown below
- Choose 3D Display Interactions. This will display interacting side chains
- Selections, Save Selections, name it Interactions
- Style, Sidechains, Stick (so next step will just color side chains)
- Color, atom
- In defined sets choose Interactions. Analysis, Label, Per Residue & No.
- Analysis, Label Scale, 3
- Style, Background, White
- 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
Instructions
- File, Retrieve by ID, MMDB
- Analysis, Seq. & Annotations, Uncheck Conserved Domains
- Analysis, Defined Sets. Click 1st domain (PH = top 3O96_A_3d_domain)
- Style, Protein, C-Alpha Trace.
- Color , Unicolor, Yellow
- Defined Sets. Choose 2st domain (N-Lobe). Color, unicolor, Cyan
- Defined Sets. Choose 3st domain (C-Lobe). Color, unicolor, Grey, Light Gray
- Seq. & Annotations, Details Tab, Uncheck Conserved Domains.
- 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.
- Select, Save Selection, CatLoop
- Color, Unicolor, Red
- Repeat for Activation Loop and save the selection. Color Unicolor, Blue
- Style, Background, White
- File, Share Link, Lifelong Short Link
Numbering or generic kinase and AKT
SITE |
Generic |
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 |
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
- File, Align, Structure to Structure
- Input 3CQW and 3O96
- Choose All Matching Molecules Superimposed
- In the top of the right hand alignment window, save the aligned state as presented (al_seq1). Just the aligned sequences will be highlighted.
- View, View Selection
- Style, Background, White
- File, Share Link, Lifelong Short Link
- Toggle between the two states by clicking the toggle menu button just underneath the File menu button