Ligand binding statistics

     The interactive statistics page provides a way to view a statistical information regarding the interaction of a ligand with respect to residues that form an environment. The environment is a set of neighbour residues that interact with the ligand through a number of interaction types. It is possible to view two sets of ligand information on the same returned graph to allow comparison of the environment of these ligands.

This page is ordered to answers the next questions:
1. Which residue type is preffered by a ligand interaction of a small molecule?
2. Within which environment in terms of residues set the specified ligand occures through out all PDB entries and how often?
3. Which pair/triple/... residues are prefferable for the ligand?
4. The above questions but regarding small molecule atoms / group of atoms, for example: adenosine group of ATP/ADP/A.

     Here we classify a residue type as amino-acid, nucleic-acid, water and ligand. This classification is parameter of distribution. The secondary structure can be specified as distribution parameter as well and it can be combined with the residue type.

     Description of a ligand follows the rules from the ligand search and has the same flexible format.

     To start search ligand statistics go to the start page of MSDsite ( http://www.ebi.ac.uk/msd-srv/msdsite and click on the line "Ligand statistics" that is in the left top coner of the page as shown on the picture below:

Let's consider particular questions that we can answer using this service.

Which small molecule residues are preffered by nucleotides such as ATP,ADP,GTP,GDP

We separate these nucleotides into two groups:
1. ADENOSINE-5'-TRIPHOSPHATE/DIPHOSPHATE: ATP,ADP
2. GUANOSINE-5'-TRIPHOSPHATE/DIPHOSPHATE: GTP,GDP

Now we can use MSDsite to answer the question.

Steps:
1. We are changing the shown on the picture fields of the statistics from:
   
2. Type ATP|ADP in the "Hetero" field of the first legend and GTP|GDP in the "Hetero" field of the second legend
3. Set up distribution to just by "Ligands". For this we switch off the check boxes "Amino acids", "Nucleic acids" and switch on the check box "Ligands".

After this modifications the form should look like:


4. Click on the "Search statistics" button and get back a distribution of ATP|ADP / GTP|GDP interactions by ligands 3 letter code.

As we can see the undoubted leader is Magnesium (MG).

Now we can question our self: which site of ATP/ADP/GTP/GDP is interacting with MG?

We can answer this question by click on the one of two bars which correspond to MG.
• Click on the first bar which corresponds to MG and ATP|ADP interactions.

This will bring us a chart of atomic bonds distrigution between ATP|ADP on the one side and MG on the other.

As can be seend from the chart the only phosphade part of ATP/ADP is involved in the interactions.

Going back (back button in the browser) to the ATP|ADP/GTP|GDP interactions chart and by clicking on the bar that corresponds to interactions between GTP/GDP and MG we are getting pretty much the same atomic bonds distribution that reveals that GTP|GDP interacts with MG by their phosphade part and all interactions are MG - Oxygen.

Within which environment in terms of residues set Magnesium as ligand occures through out of all PDB entries and how often?

To answer the question we set up the statistics form as shown on the picture:

I.e. we
• change "Distributed by" to "all residues"
• switch on "Amino acid", "Nucliec acids", "Ligands" and "Water" check boxes
• type MG in the field "Hetero".

Now by click on the "Search statistics" button we get back the chart that is answer to the question above.

Let's explore this chart little bit more consider the environment:
GLU GLU HIS HOH HOH HOH

• Click on the bar that corresponds to the environment
  GLU GLU HIS HOH HOH HOH

As a respond the service brings back a list of PDB entries that have MG within this environment.

• In the list of PDB entries choose the first one (1jz7) by click on the link in the column "ID" as shown on the picture:
  
• The detail page "Bound molecules" contains matched search criteria ligands at the top of the bound molecules list. Note:
  The search criteria was:
  • ligand: MG
  • environment: GLU GLU HIS HOH HOH HOH
  • environment matches exactly, i.e. these are the only residues in the ligands environment, no less and no more.
• Click on the link under image if you have a Rasmol script application setted up for mime-type: application-x/rasmol or go to the link under image to load the structure in the viewer applet. Rasmol gives a picture something like below:
  

Here we can see MG octahedral metal coordination formed by three water molecules, two Glutamic acids and one Histidine.

Compare Adenosine and Guanozine amino-acids binding properties?

Using MSDchem service we can obtain necessary information about ligands that contain these groups and their atoms names.

Adenosine is contained in ATP,ADP,A chemical compounds and is described by atoms N1,N3,N6,N7,N9,C2,C8 (other carbons are well hidden and not active).

Guanozine is contained in GTP,GDP,G chemical compounds and is described by atoms N2,N1,N3,N7,N9,O6,C8 (other carbons are well hidden and not active).

Perform the next steps to get the answer:
1. Fill the statistics from as shown on the picture below:
   
   
   • Distribution is by 1 residue and only by amino-acids (all other check boxes in this line are off).
   • In the "Hetero" field for legend 1 type:ATP|ADP|A.N6|N1|N3|N7|N9|C2|C8
   • In the "Hetero" field for legend 2 type:GTP|GDP|G.N2|N1|N3|N7|N9|O6|C8
2. Click on the "Search statistics" button to get the result chart.
3. As can be seen from the chart Adenosine have much more hydrofobic interactions rather then Guanozine. Looks like Guanozine is polarized.

Now let's explore the interactions in more details.

4. Click on the red bar that corresponds to Glutamic acid (GLU)

this brings the atomic bonds distribution between Adenosine and Glutamic acid

As can be seen from this chart Adenosines atom N6 is the absolute leader in interactions with Glutamic acid and most interactions are Hydrogen bonds. Moreover a lot of interactions are with Glutamic main chain atom O.

5. Go back to the comparison of Adenosine and Guanozine chart.
6. At this time click on the green bar that corresponds to Glutamic acid (GLU)

this brings the atomic bonds distribution between Guanozine and Glutamic acid

7. As can be seen from this chart Guanozine atoms N1,N2 are most active in interactions with Glutamic acid and most of the interactions are Hydrogen bonds. Even more, most of the interactions are with the pair of Glutamic atoms OE1, OE2.

Let's find out which site of Guanozine is most biologically active.

8. For this purpose we clean up the "Residue" field in the atomic bonds statistics form as show on the picture below:
   
9. Click "Search" button and get back the distribution of Guanozine atomic bonds across all amino-acids.
10. As can be seen from the chart the biologically active part of Guanozine is formed by atoms: N1,N2,O6.

Now let's consider what is happening in 3D

11. Click on the first yellow bar that corresponds to hydrogen bond interactions between GDP.N1 and ASP.OD1

This will bring us a list of PDB entries that correspond to hydrogen bond interactions between GDP.N1 and ASP.OD1

Let's go into detail pages of these PDB entries starting from the first one. We will add all matched ligands from these detail pages to the Multi-View page.

12. Click on the first link in "ID" column:
    
    

    The detail page presents interactions of the ligands on the residual level.

    Now we are going to add the ligand to the Multi-View page for comparison of binding properties in 3D.

    Note:
    If you have the Multi-View page opened in your browser then you should clean it up.
    Multi-View window is ordinary browser window with the reserved name. If you have not use Multi-View service with MSDsite then you wont have this window opened.
13. Switch on the check box that corresponds to the matched search criteria GDP ligand:
    
14. Click the button "Add to the multi-view page..."

    Note:
    If you've done it for the first time during the session then a new browser window will be opened, otherwise the information about the ligand occures in the existing window.

15. Repeate the last three steps for another four next in the list PDB entries:
    

Now let's have a look what we supposed to have on the Multi-View page:


16. To get 3D view of aligned ligands with their environment we switch on all check boxes as shown on the picture above.
17. On the top of the page where "View in:" is written there are links to the two of visualisation tools: Rasmol and AstexViewer. Click on the link under image if you have a Rasmol script application setted up for mime-type: application-x/rasmol or go to the link under image to load the structure in the viewer applet. Rasmol gives a picture something like below:
    
    

    After zooming the view we get a more clear picture about what is happening between Guanozine atoms N1,N2 and Aspatic acid atoms OD1,OD2. It is bidentide Hydrogen bond interaction: