[ PDB Search | Convert | Display Hydrogen Bonds | Crystallographic Analysis Tools | PDB Preparation - Symmetry | PDB Preparation - Occupancy | PDB Preparation - Alternative Orientation | Biomolecule ]

23.3.1 PDB Searching

Step 1: Use the search tab to search for a PDB by a string e.g. kinase or the pdb code: 1xbb. The table can be sorted and filtered by right clicking on the column header. A hyperlink to the PDB website is provided for each entry.

Step 2: Scroll along the table to find out more information such as resoultion (res), hetero atoms (het) and a direct link to the Uniprot website.

Step 3: Double click on the table to load and display the pdb structure.

23.3.2 Converting a PDB File into an ICM Object

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.

Step 1: Read in a PDB file and then right click on the pdb name in the ICM Workspace and choose the option "Convert PDB".

Step 2: Note the new object will have "ICM" next to its name in the ICM Workspace. Also a log of the changes made are listed in the terminal window.

23.3.3 How to display 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.

• As an example we will use the PDB structure 1STP. Type 1STP in the pdb search tab and press return.
• In order to display energy related properties we need to convert the PDB file into an ICM object. To convert 1STP into an ICM object follow the instructions Converting a Protein into an ICM Object. In this example, the option "Replace the Original" was selected.
• Display the receptor in wire format and the ligand in xstick.
• Right click on the ligand and select "Neighbors" - Enter 3 Angstroms and Type = Visible. Do not exclude source (the ligand) therefore remove tick from box entitled "exclude source".
• Select the display tab and then select the Display H-Bond button.

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

23.3.4 Protein Preparation and Crystallographic Analysis Tutorial

23.3.5 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

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.

• Use the PDB search tab to load the crystal structure 1cdg.
• Inspect the ligand binding pocket of maltose (mal)
• To identify if there are any other chains involved in the interaction with the ligand select the whole structure in the ICM Workspace.

• Tools/Crystallographic Neighbor
• Select a 7A radius
• Check "create symmetry related molecules" and "display symmetry neighbors".
• Inspect the neighbors surrounding maltose(mal). Each symmetry related subunit can be colored by object by clicking and holding the representation button in the display tab and selecting color-by.

23.3.6 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

• Type in the PDB search tab 1atp and the structure will be displayed in the graphical display.
• Use the ICM workspace to undisplay everything except for the "e" subunit. You can do this by clicking in the blue boxes in the ICM Workspace.
• Display the "e" subunit in wire representation using the wire button in the display tab.
• Click and hold on the wire button and select Color-by B-Factor. Regions of high B-factor are colored red.

23.3.7 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.

23.3.8 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

• Read and load the PDB file 1DWN
• Tools/Xray/Biomolecule Generator
• Tick the makeAllBiomolecules box (Warning this may take a few minutes to generate)
• The generated molecules will be listed in the ICM Workspace. Each one can be selected and displayed. The biomolecule is shown below.

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