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iCn3D Skill: Selection through Sequence and Annotations

Last updated

Jan 9, 2025
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- iCn3D Skill: Mutations
- iCn3D Skill: Showing a Protein-Protein Interface

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Structure

MMDB ID: 1xww
Protein: Low molecular weight protein tyrosine phosphatase
Activity: hydrolyzes Tyr-OPO₃²^- phosphoester bond
Description: single chain, bound SO₄²^- (competitive inhibitor), bound glycerol (nonspecific stabilizer)

Load Structure and Mouse/Trackpad Controls

Open iCn3D - https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html
For a simple menu, use the dropdown: File > Customize Menus > Simple Menus.
In the Please input MMDB or PDB, enter 1xww. Press enter or click load biological unit.
Default render is ribbon (cartoon) with black background and small molecules shown as sticks. Hover over objects with the mouse to reveal their identity.

Figure: The Sequences and Annotations Menu

For this part, we will be using the model from Activity 1. To load the premade model from Part 1, use this link: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?CgfEnF27TN7aYQpr6

From the literature, it is known that the active site is a nucleophilic cysteine (C12). It is part of the phosphate-binding loop (P-loop, AA 12-18: sequence CLGNICR). Let’s find, select, and render these amino acids.

Modeling Instructions

Under Analysis (top menu bar), choose Sequence and Annotations
Choose Details tab, uncheck Conserved Domains

Before we continue, look at the built-in choices you have for selection:

In the Sequences and Annotation window, click Protein 1XWW_A
Under Select (top menu bar), choose Toggle Highlights
Hover over C12 in the sequence (in Seq and Annot window), click and hold down the mouse key, and sweep over C12-C18 to select the P loop
Select, Save Selection, name it: Ploop
Within this highlighted selection, Style, Side Chains, Sticks
Color, Atom
Analysis, Label, Per Residue & Number
Analysis, Label Scale, pick number that works for you
Analysis, Label, Change Label Color (globally). Click in the text box and a Color box will pop up, choose from a palette, then Display. (Alternatively, pick a hex code).
In the Sequences and Annotation window, click SO4
Style, Chemicals, Sphere to change the sulfate to a space filling rendering
Files, Share Link, Copy Short URL

Pre-Rendered Model Link

To check your work (or if you got stuck during any of the steps above) catch up using this link: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?QhtGuE8pkaJpGs1X9

Note: For some enzymes, iCn3D can automatically display key active site and binding residues. These can be seen as shown by selecting the items indicated in the left figure.

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