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22.3 Protein Structure Tutorials
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[ PDB Search | Convert | Ligand Binding Pocket Analysis | Ligand Pocket | Pocket Conservation | Displaying Key Hydrogen Bonds | Crystallographic Analysis Tools | PDB Preparation - Symmetry | PDB Preparation - Occupancy | PDB Preparation - Alternative Orientation | Biomolecule ]

Overview

This lesson will take you through the basics of reading and displaying PDB structures and their conversion into ICM objects. Topics covered include:

22.3.1 PDB Searching


Objective

To display the crystal structure of a G-Protein Coupled Receptor (GPCR).

Background

Using ICM it is easy to quickly search and download PDB files using the .pdb search. tab.

Instructions

  1. Click on the PDB Search Tab
  2. Type bovine rhodopsin into the search box and click the button next to it. A table of hits will be displayed at the bottom of the GUI.
  3. Double click on the ID field of structure 1F88 to display the structure.

Notes and things to try:

Manual References (Web Links)

Finding a PDB Structure

22.3.2 Converting a PDB File into an ICM Object


Objective

To convert a PDB file into an ICM object.

Background

Sometimes it is necessary to have a PDB file in the form of an ICM molecular object. For example, it's a convenient way to list and/or to change a torsion angle (or a series of them). It is also necessary to convert PDB files into ICM objects for ICM functions such as docking. There are two principally different modes of conversion. In the default mode the program looks at the residue name and tries to find a full-atom description of this residue in the icm.res file. This search is suppressed with the exact option. Hydrogen atoms will be added if the converted residues are known to the program and described in the icm.res library.

Instructions

To convert a PDB file into an ICM object (**IMPORTANT Do not use this method for small molecules (sdf, mol, mol2) use MolMechanics/ICM-Convert/Chemical) :

Notes and things to try:

22.3.3 Ligand Binding Pocket Analysis Examples


The examples covered here include:

Displaying only the residues that surround the ligand binding pocket.

Displaying sequence conservation around the ligand binding pocket

Displaying hydrogen bonds between a ligand and the receptor

22.3.4 Displaying only the residues that surround the ligand binding pocket.


There is a quick and easy way to do this as described in the Tips section of the manual entitled "Quick Binding Pocket Display" or you may want to follow the instructions below for a more user-defined method.

For example if your structure is shown in ribbon you and you wanted to display the surrounding residues in xstick and udisplay the rest of the structure you would do the following.

Steps shown graphically below for the kinase 1ql6 and the atp ligand.

Step 1: Receptor (1ql6.a) is in ribbon display:

Step 2: Double click and select the atp molecule in the ICM Workspace

Step 3: Right click on the selected atp molecule in the ICM Workspace and select Neighbors. Enter radius and type of selection. Click OK and you will see a graphical selection of green crosses around the pocket.

Step 4: Convert your selection to a residue selection if you wish. You will then see green "R" in the graphical selection rather than green crosses.

Step 5: Select the xstick representation and the residues around the ligand will be displayed.

Step:6: If you want to undisplay the rest of the receptor outside the pocket use the invert selection button and then click the ribbon representation button.

22.3.5 Displaying the sequence conservation around the ligand binding site.


Here is an example on how to superimpose the structures of two proteins and display the sequence conservation around the ligand binding pocket.

PDB Search

NOTE: Please note that all alignments are linked with structure therefore selections can be made in the alignment. Also as an example structure can be colored according to the color in the alignment which is useful for identifying conserved regions.

22.3.6 Displaying hydrogen bonds between a ligand and receptor.


NOTE: The method by which hydrogen bonds are calculated is described here in the command line manual. The GRAPHICS.hbondMinStrength parameter determines the hbond strength threshold for hbond display. The strength value is between 0. and 2. By changing 1. to 0.2 you will see more weak hydrogen bonds.


NOTE: Different options for displaying the H-bond can be accessed by clicking and holding on the H-bond button in the "Display" tab.

22.3.7 Protein Preparation and Crystallographic Analysis Tutorial


22.3.8 PDB Preparation - Symmetry


Background When inspecting a ligand binding pocket it is important to check that the true pocket is formed by chains which are not explicitely present in a PDB entry. Therefore it is necesary to use Tools/X Ray/Crystallographic Neighbor to find all molecules/subunits or chains involved in the interaction with the ligand. Molecular objects and 3D density maps may contain information about crystallographic symmetry. It consists of the following parameters:

  1. Crystallographic group eg. P2121 that determine N (depends on a group) transformations for the atoms in the asymetric unit.
  2. Crystallographic cell parameters A, B, C, Alpha, Beta and Gamma
To generate the coordinates within one cell one needs to apply N transformations and then to generate neigboring cells the content of one cell needs to be translated in space according to the cell position.

Example As an example let us look at Cycloldextrin glycosyltransferase (PDB Code: 1CDG). The problem with docking to this receptor is that the true pocket is formed by chains which are not explicitly present in the PDB entry. Site mb1 includes serine 382. This cannot be predicted just by looking at the structure. Therefore we need to identify symmetry related molecules to this protein.

22.3.9 PDB Preparation - Occupancy and B-Factors


Background When preparing a PDB for analysis (eg docking or modeling) it is important to check the reported occupancies and b-factors. The occupancy is a fraction of atimic density at a given center. If there are two eqally occupied conformers both will have an occupancy of 0.5 - the normal value is 1 range 0-1. The *{B-Factor} is the mean-square displacement of atom from its position in the model - the normal range is 5-50.

One way of visualizing the occupancy and b-factor is by coloring the structure by these values. You can do this by clicking and holding on a representation button in the display panel and selecting Color-by.

As an example let us look at the crystal structure 1ATP

22.3.10 PDB Preparation - Residue Alternative Orientation


For some very high resolution structures two alternative conformations for a residue are provided. Therefore for docking you need to decide to use one conformation of the residue or generate seveal separate docking models. This could be performed using multiple receptor conformation docking.

Here is an example of alternative residue orientations found in a crystal structure of a Fatty Acid Binding protein in complex with stearic acid.

22.3.11 Biomolecule Generator


Objective

Here we will investigate the biological environment of a virus protein . PDB code 1DWN.

Background

It is very useful to know how a protein from the PDB may look in a biological environment. The PDB entries solved by X-ray crystallography and deposited in the PDB contain the information about the crystal structure rather than the biologically relevant structure. For example, for a viral capsid only one instance of capsid protein complex will be deposited and only one or two molecules of haemoglobin that is a tetramer in solution maybe deposited. In some other cases the asymmetric unit may contain more than one copy of a biologically monomeric protein. ICM reads the biological unit information and has a tool to generate a biological unit. Not every PDB entry has the biological unit information.

Instructions

NOTE: Please note that right clicking on a PDB file in the ICM Workspace will tell you whether there is any Biomolecule information available for the structure. If this information is not present then the option will be greyed out.

Manual References (Web Links)

Biomolecule Generator


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