Download What is pdb file and how to view it? The Protein Data Bank (Pdb

What is pdb file and how to view it?
The Protein Data Bank (Pdb) format file is used to represent the threedimensional macromolecules structure such as proteins and nucleic acids
obtained by X-ray crystallography or NMR spectroscopy for do a different
analysis for theses molecules. The structure files can be viewed by open
source computer programs such as RasMol. It is the open-source
program for visualization of proteins, nucleic acids, and small organic molecules.
The following steps you will learn how to
get pdb file structure from the websites are more commonly used and then
interprete it using RasMol program (It is divided
into two windows: Display window (See the molecule here) & RasMol Command
Window (Write the command here to
display the molecule).
How to get the pdb file and how to analyze it?
1. Getting the pdb file for small molecules
2. Getting the pdb file for nucleic acids
3. Getting the pdb file for enzymes (Proteins)
4. Getting the pdb file for Protein-DNA complex
How to transfer a structure drawing from Symys Draw to RasMol?
A. Draw any structure in the Symyx Draw.
B. Save the structure as skc file.
C. Open the RasMol program and from File menu choose Open, then click
on the Protein Databank button beside the
field of File name and pull down the menu next the button to MDL Mol File
Format.
Getting the pdb file for small molecules
Screenshot of Ascorbic acid using RasMol program
A. Get the Vitamin C pdb file:
1. Go to Molecular models website.
2. Select the Natural product > Ascorbic acid > On the image right-click on mouse > Vit-C > View
> vit-c.pdb
B. Open the pdb file with RasMol & learn how to manipulate the molecule:
1. You can see the content of pdb file with text editors such as Notepad, Wordpad, or MS Word.
2. Go to file in the RasMol program > Information to get the number of groups, atoms, and bonds of
the molecule.
3. Rotate the molecule (X,Y) by clicking the left mouse and translate (move) it to other location of the
screen by clicking
the right mouse
4. Zoom in and out the molecule by holding the SHIFT-left click on mouse, then the cursor move to up
(Zoom in) and move
to down (Zoom out).You can change magnification of the image by typing in the RasMol Command
Window "zoom 80".
5. Rotate the molecule (Z) by holding the SHIFT-Right-click on mouse and then move the cursor left
and right.
6. Type in the RasMol Command Window "reset" to restores the molecule to center of rotation i.e. the
original viewing.
7. See the image as slab by holding the the Ctrl key with left-click on mouse.
8. To color background, type in the RasMol Command Window: background white.
9. See the structure with different display representations by clicking Display > Wireframe or Sticks.
10. Copy a graphical file by clicking Edit > Copy which paste into MS Word or from Export > GIF to
save it on your
computer and then paste into MS Word.
11. Delete the currently molecule for import another molecule to program by typing in the RasMol
Command Window: zap.
C. Analysis and interpretation the Ascorbic acid structure:
1. How to differentiate between different types of atoms?
Coloring atoms:
Each atom in the molecule show a different color: Carbon (Grey), Hydrogen (White), and Oxygen
(Red) as the CPK
color scheme.
Label the selected atom:
To label the selected atom, go to Settings > Pick Label > Click on the atom > The number ID of
atom will appear
for example, C10 (C: Atom name, 10: Serial number of atom). If you Go to Settings > Pick Ident >
click on an atom >
the atom number ID will appear in the RasMol Command Window.
2. How to label all atoms and how to remove it?
- To label all atoms, type in the RasMol Command Window:
RasMol> set picking label
RasMol> label
RasMol> color labels white
RasMol> set fontsize 20
RasMol> label off
3. How to choose a particular atom?
To select the preferred atoms like oxygen, type in the RasMol Command Window: select oxygen
and type in a new
command line: color red.
4. How to measure the distance between two atoms?
- To show a label the distance between the atoms in Angstroms (Å) (1 nanometer = 10 Angstroms).
Type in the RasMol Command Window: set picking distance. When pick between the two atoms,
the information will
appear in the command line and the distance between two atoms will be shown in molecule.
- To show the information in the display window, type in the RasMol Command Window: set
picking monitor.
- To remove the distance monitors in the display window, type in the RasMol Command Window:
monitor off.
5. How to measure the angle bond between three atoms?
Type in the RasMol Command Window: set picking angle. When pick between the three atoms, the
information will
appear in the command line and the distance between three atoms will be shown in molecule.
6. How to measure the angle bond between four atoms?
Type in the RasMol Command Window: set picking torison. When pick between the four atoms, the
information will
appear in the command line and the distance between four atoms will be shown in molecule.
7. How to save the selected atoms?
To save the selected atoms as pdb file Type in the RasMol Command Window: save {pdb}
<filename>.
8. How to save the sequence of commands and how to restore to see them again?
Type in the RasMol Command Window: save script <filename> or save
rasmol <filename>. To see the molecule later, open the PDB file for the molecule and then type in
the RasMol
Command Window: script <filename>. You can read and edit a script (The information contained in
the file) with any
word processor.
(Hint: You can't undo the command in the RasMol program).
Click here to learn more information about RasMol program.
Other links:
Structures of Inorganic Crystals
Getting the pdb file for nucleic acids
Screenshot of B-DNA using RasMol program
A. Get the B-DNA pdb file:
1. Go to Nucleic acids databases (NDB) website.
2. Type in the blank field next to search NDB ID BDL001.
3. The new page will load. In the end of this page, click on The Protein Data Bank: 1BNA to open
another site (RCSB
Protein Data Bank). Above the B-DNA image click on Download files and select PDB File
(Text) to get pdb file.
B. Open the pdb file with RasMol & learn how to manipulate the molecule:
1. You can see the content of pdb file with text editors such as Wordpad or MS Word.
2. Go to file in the RasMol program > Information to get the number of groups, atoms, and
bonds of the molecule.
3. Rotate the molecule (X,Y) by clicking the left mouse and translate (move) it to other location
of the screen by clicking
the right mouse
4. Zoom in and out the molecule by holding the SHIFT-left click on mouse, then the cursor move
to up (Zoom in) and move
to down (Zoom out).You can change magnification of the image by typing in the RasMol
Command Window "zoom 80".
5. Rotate the molecule (Z) by holding the SHIFT-Right-click on mouse and then move the cursor
left and right.
6. Type in the RasMol Command Window "reset" to restores the molecule to center of rotation
i.e. the original viewing.
7. See the image as slab by holding the the Ctrl key with left-click on mouse.
8. To color background , type in the RasMol Command Window: background white.
9. See the structure with different display representations.
10. Copy a graphical file by clicking Edit > Copy which paste into MS Word or from Export > GIF
to save it on your
computer and then paste into MS Word.
11. Delete the currently molecule for import another molecule to program by typing in the
RasMol Command Window: zap.
C. Analysis and interpretation the B-DNA structure:
1. How to differentiate between different types of atoms?
Coloring atoms:
Each atom in the molecule show a different color: Carbon (Grey), Hydrogen (White), Oxygen
(Red), Nitrogen (Blue), and
Phosphorus (Orange) as the CPK color scheme.
Label the selected atom:
Go to Settings > Pick Label > click on an atom > the atom number ID will appear for example
DC11A.N1 (Group
Deoxcytosine (Group DC), serial number of group: 11, Chain A, Atom name: Nitrogen, Serial
number of atom no. 1).
If you Go to Settings > Pick Ident > click on an atom > the atom number ID will appear in the
RasMol Command
Window.
2. What is the sequence of the DNA?
. Type in the RasMol Command Window: show sequence.
3. What many chains in the DNA and how to select the particular chain?
- Type in the RasMol Command Window: show selected chains to show all chains in the DNA.
- Type in the RasMol Command Window: select *a. Go to the Display > Stick and then Colours
> Chain.
4. How many nucleotides (Purines or Pyrimidines) in the DNA?
- In the RasMol Command Line, type: select purines. Go to the Display > Ball & Stick to show
only purines.
- In the RasMol Command Line, type: select pyrimidines. Go to the Display > Ball & Stick to
show only pyrimidines.
5. How many complementary bases (AT or CG) in the DNA?
- In the RasMol Command Line, type: select at. Go to the Display > Ball & Stick and type in a
new command line:
color green to show only AT bases as solid spheres.
- In the RasMol Command Line, type: select cg. Go to the Display > Ball & Stick and type in a
new command line:
color green to show only CG bases as solid spheres.
6. How to see only AT or CG complementary bases?
In the RasMol Command Line, type: restrict at. Go to the Display > Ball & Stick.
7. How many each base (T, A, C, or G) in the DNA?
Type in the RasMol Command Line: select DT. Go to the Display and choose Ball & Stick to
show only thymine bases
and type in a new command line: color green or any color to show only DT bases.
Repeat type the command as above for other bases.
8. How to differentiate between different types chains?
Go to the Colours and choose the Chain or go to the Display, choose Backbone and then
from Colours > Chain to
see the different colors of the DNA chains.
9. How to select hetero atoms?
Heter atoms: Ligand or solvent (Water or ions), type in the RasMol Command Window: select
oxygen. Go to the
Display and choose Spacefill to see only the oxygen from water as solid spheres (Red color).
10. How to see the hydrogen bonds between the phosphorous atoms of the nucleic acid?
Type in the RasMol Command Window: set hbond backbone and type in a new command
line: hbond.
11. How to save the selected atoms?
To save the selected atoms as pdb file Type in the RasMol Command Window: save {pdb}
<filename>.
12. How to save the sequence of commands and how to restore to see them again?
Type in the RasMol Command Window: save script <filename> or save
rasmol <filename>. To see the molecule later, open the PDB file for the molecule and then
type in the RasMol
Command Window: script <filename>. You can read and edit a script (The information
contained in the file) with any
word processor.
(Hint: You can't undo the command in the RasMol program).
Click here to learn more information about RasMol program.
Getting the pdb file for enzymes (Proteins)
Screenshot of Horse Liver Alcohol Dehydrogenase Apoenzyme using RasMol program
A. Get the Horse Liver Alcohol Dehydrogenase Apoenzyme pdb file:
1. Go to International Union of Biochemistry and Molecular Biology website.
2. Click EC 1 Oxidoreductase > up to 50 below Enzyme file type > EC 1.1.1 With NAD+ or
NADP+ as acceptor > EC
1.1.1.1 alcohol dehydrogenase > EC 1.1.1.1 to see more information about enzyme.
3. Go to RCSB Protein Data Bank website and type in the blank field next to search PDB ID: 1YE3, the
new page
will load. Click on molecule to see all information about this enzyme then click on Download files and
select PDB File
(Text) to get pdb file.
4. In the end of page of the Horse Liver Alcohol Dehydrogenase Apoenzyme, see the Ligand Chemical
Component. Below
the Ligand Chemical Component click on Ligand Explorer to view interactions between
macromolecule-ligand.
B. Open the pdb file with RasMol & learn how to manipulate the molecule:
1. You can see the content of pdb file with text editors such as Wordpad or MS Word.
2. Go to file in the RasMol program > Information to get the number of groups, atoms, and bonds of
the molecule.
3. Rotate the molecule (X,Y) by clicking the left mouse and translate (move) it to other location of the
screen by clicking
the right mouse
4. Zoom in and out the molecule by holding the SHIFT-left click on mouse, then the cursor move to up
(Zoom in) and move
to down (Zoom out).You can change magnification of the image by typing in the RasMol Command
Window "zoom 80".
5. Rotate the molecule (Z) by holding the SHIFT-Right-click on mouse and then move the cursor left
and right.
6. Type in the RasMol Command Window "reset" to restores the molecule to center of rotation i.e. the
original viewing.
7. See the image as slab by holding the the Ctrl key with left-click on mouse.
8. To color background , type in the RasMol Command Window: background white.
9. See the structure with different display representations.
10. Copy a graphical file by clicking Edit > Copy which paste into MS Word or from Export > GIF to
save it on your
computer and then paste into MS Word.
11. Delete the currently molecule for import another molecule to program by typing in the RasMol
Command Window: zap.
C. Analysis and interpretation the Horse Liver Alcohol Dehydrogenase Apoenzyme structure:
1. What is the sequence of the amino acids that present in protein?
.
Type in the RasMol Command Window: show sequence.
2. How to get a certain type of amino acids?
- To show only acidic amino acids, type in the RasMol Command Window: select acidic and then go
to the Display >
Ball & Stick or type in the RasMol Command Window: select amino and not (basic or
neutral) then go to the
Display > Ball & Stick.
- To show only acyclic amino acids, type in the RasMol Command Window: select acyclic and then
go to the Display
> Ball & Stick.
3. How many the polypeptide chains in the enzyme?
Type in the RasMol Command Window: show selected chains to show all chains that include the
complex and then
go to Display > Sticks (Shows the bonds and atoms in stick)
4. How many the amino acids in the chain A of the enzyme?
Type in the RasMol Command Window: select *.ca and *a (Select all Alpha carbon (CA) atom on
chain A).
5. What is the N and C-terminal of amino acids in chain A?
Type in the RasMol Command Window:
RasMol > select 1,374 and *.ca and *a
RasMol > label
RasMol > spacefill 400
6. How to see the secondary structure (Helix, Sheet, and turn) of the enzyme?
Type in the RasMol Command Window: select helix and then go to Colours > CPK to show the
helix as magenta
color.
Type in the RasMol Command Window: select sheet and then go to Colours > CPK to show the
sheet as yellow
color.
Type in the RasMol Command Window: select turn and then go to Colours > CPK to show the
sheet as pale blue
color and determine the amino acid per turn.
7. How to select hetero atoms?
Heter atoms: Ligand or solvent (Water or ions).
- Select water by typeing in the RasMol Command Window: select hoh (The hydrogen is not
included) and then go to
the Display > Spacefill and then from Colours > CPK.
- Select ligand by type in the RasMol Command Window: select ligand and then go to the Display >
Spacefill then
from Colours > CPK to show the cofactors, protheic groups, or inhibitors bonded to enzyme.
- To restrict ligand, type in the RasMol Command Window: restrict ligand and label it by typing in
the RasMol
Command Window: label %a%c%n%r (%a: Name of atom, %c: Chain Identifier, %n: Name of residue, and %r:
Number of residue).
8. Where is the disulphide bonds of the protein molecule in the complex?
Type in the RasMol Command Window:
RasMol > select cys (Show the atoms number of cysteine residues that form part of a disulphide
bridge).
RasMol > set ssbond, then go to the Display > Ball & Stick.
9. How to get the codes amino acids?
Type in the RasMol Command Window: ?Amino acid codes.
10. How to save the selected atoms?
To save the selected atoms as pdb file Type in the RasMol Command Window: save {pdb}
<filename>.
11. How to save the sequence of commands and how to restore to see them again?
Type in the RasMol Command Window: save script <filename> or save rasmol <filename>. To
see the molecule
later, open the PDB file for the molecule and then type in the RasMol Command Window: script
<filename>. You
can read and edit a script (The information contained in the file) with any word processor.
(Hint: You can't undo the command in the RasMol program).
Click here to learn more information about RasMol program.
Other links:
- Enzyme database
- Functional Coverage of the Proteome