E. coli Adk (PDB: 2ECK)
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Description
E. coli AMP kinase. The adenyl nucleobase is held in place firmly. A diamine purine, with an amine at the C2 atom is unlikely to fit due to the backbone ketone of valine-59.
About
This protein view was generated using Michelanglo.
About
Michelaɴɢʟo is an accessible and open-source web-based application which supports the generation, customisation and sharing of interactive three-dimensional macromolecular visualisations for digital media without requiring programming skills. PyMOL file, PDB file, PDB identifier code or protein/gene name can be provided which form the basis of visualisations using the NGL JavaScript library. Hyperlinks that control the view can be added to text within the page. Protein coding variants can be highlighted to support interpretation their potential functional consequences. The resulting visualisations and text can be customised and shared, as well as embedded within existing web sites by following instructions and using a self-contained download.
Protein basics
Proteins are chains of L-amino acids linked via their backbone atoms (carboxyl and amine of the α carbon). This sequence of backbone atoms is represented by the (green) ribbon-like structure.
When the backbone atoms hydrogen-bond with each other in a consistent way secondary structure arises.
α-Helices are represented as spirals, while β-sheets appear as adjecent flat strands.
Some residues of interest are represented as ball and sticks like akin to an old chemistry set. In these representations the atoms are colour-coded based on the element. Carbon can be any colour, while nitrogens are in blue, oxygens are in red, hydrogens in white, sulfurs in yellow and phosphorous in orange. The latter is found as phosphate groups so will appear as a distinctive red-tipped orange tetrahedral end of a sidechain. Ions are represented by a variety of colours. But are generally represented as spheres of the correct atomic radius.
View builder
This tool allows you to create custom anchor elements that control the protein. See documentation for more.
<span class="prolink" data-toggle="viewport">Change a setting!</span>Selection
Option A. Selection language
For more information on the NGL selection language see NGL manual
This controls the residues to focus on. The selection uses the NGL selection language. 1:A will select residue 1 of chain A, 1-20:B the residues 1 to 20 of chain B, * for everything, PLP (or [PLP]123:D) will select the residue named PLP (a ligand).
The logical operators and and or can also be used, e.g. :B or :C will select chains B & C. You can only select residues that exist in the structure, if not it will either show all or erroneously pan off camera when manually written. In this builder you will not be allowed to.
Also to prevent memory issues in mobiles the limit, in the builder only, for residue mode is 500 atoms.
To select two different elements use the logical operator or, not and, because you want to select anything that matches X or Y.
Option B. Build Selection
The following is simpler, but much more limited that the previous.
or
What to show residue and not the domain, or vice-versa? For the full list close this, and select the appropriate focusing mode (labelled "zoom to").
Instruction
Add structure from another pages
A single page can support multiple models, which can be toggled via data-load in the prolink (a link that control the protein view).
To show a structure, two pieces of information are needed:
- one is the structure, namely the information of each atom (e.g. element, residue, coordinates). The PDB file basically.
-
the other is the representation, namely the combination of the orientation, residues shown, colors and field of view etc. In the case of PyMOL generated views,
these are functions that can be called via the attribute
data-view="name_of_function".
To combine two PyMOL representation of the same structure use the add representation only button: there is no need to slow things down by loading the same coordinates, else add both.
This applies also to cases where the structure is taken remotely (e.g. PDB database).
Note that editing the JS in blocked for regular users (due to security concerns), please speak to the site admin if you would like to alter your permissions. Also note that this page will refresh in order for the changes to be made.
Mutate
Create a second structure where a set of amino acids are replaced using PyMOL's mutagenesis algorithm. This will alter only the side chain of the residues mutated and does not repack the neighbouring sidechains nor does it account for blackbone torsion. Note that this page will reload for the changes to be made, so make sure you have saved the edits to the text beforehand.
View builder for loading
This tool allows you to alter the initial view of the protein that is seen once it is loaded. See documentation for more.