Proteopedia - User contributions [en]

S347/Visualising protein structure

2010-10-20T08:22:27Z

Eleanor Crabb:

== Visualising Protein Structure ==
<applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />This page is designed to be an introduction to protein structure and the 3D visualisation package, '''Jmol''', used here in Proteopedia and also on the RCSB Protein Data Bank website to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of a zinc-containing enzyme with the pdb code '''1z3a'''. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html] for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule. (The popup button will open a resizable Jmol representation of the molecule in another window.)

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the backbone of the protein will show the constituent residues in the chain.

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space-filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see the atoms in the protein.

Now, let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

[[S347/The_four_tiers_of_protein_structure|Next page - The four tiers of protein structure]]

S347/Visualising protein structure

2009-10-20T16:22:56Z

Eleanor Crabb: New page: == Visualising Protein Structure == <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />This page is designed to be an introduction to protein structure and the 3D v...

== Visualising Protein Structure ==
<applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />This page is designed to be an introduction to protein structure and the 3D visualisation package, '''Jmol''', used here in Proteopedia and also on the RCSB Protein Data Bank website to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of a zinc-containing enzyme with the pdb code '''1z3a'''. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym] for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule. (The popup button will open a resizable Jmol representation of the molecule in another window.)

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the backbone of the protein will show the constituent residues in the chain.

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space-filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see the atoms in the protein.

Now, let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

[[S347/The_four_tiers_of_protein_structure|Next page - The four tiers of protein structure]]

S347/The four tiers of protein structure

2009-10-20T16:20:51Z

Eleanor Crabb:

== The four tiers of protein structure ==

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/4'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/4'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/2'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

Eleanor Crabb/The four tiers of protein structure

2009-10-20T16:15:26Z

Eleanor Crabb: Eleanor Crabb/The four tiers of protein structure moved to S347/The four tiers of protein structure: To allow our students of the Open University course S347 to find the correct page.

#REDIRECT [[S347/The four tiers of protein structure]]

S347/The four tiers of protein structure

2009-10-20T16:15:26Z

Eleanor Crabb: Eleanor Crabb/The four tiers of protein structure moved to S347/The four tiers of protein structure: To allow our students of the Open University course S347 to find the correct page.

== '''The four tiers of protein structure''' ==

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/4'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/4'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/2'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Visualising protein structure

2009-10-20T15:57:15Z

== Visualising Protein Structure ==
<applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />This page is designed to be an introduction to protein structure and the 3D visualisation package, '''Jmol''', used here in Proteopedia and also on the RCSB Protein Data Bank website to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of a zinc-containing enzyme with the pdb code '''1z3a'''. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym] for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule. (The popup button will open a resizable Jmol representation of the molecule in another window.)

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the backbone of the protein will show the constituent residues in the chain.

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space-filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see the atoms in the protein.

Now, let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

[[Eleanor_Crabb/The_four_tiers_of_protein_structure|Next page - The four tiers of protein structure]]

User:Eleanor Crabb/The four tiers of protein structure

2009-10-20T15:52:26Z

Eleanor Crabb: New page: == '''The four tiers of protein structure''' == We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' si...

User:Eleanor Crabb/Sandbox 1

2009-10-20T15:41:09Z

Eleanor Crabb:

== Visualising Protein Structure ==
<applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />This page is designed to be an introduction to protein structure and the 3D visualisation package, '''Jmol''', used here in Proteopedia and also on the RCSB Protein Data Bank website to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of a zinc-containing enzyme with the pdb code '''1z3a'''. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym] for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule. (The popup button will open a resizable Jmol representation of the molecule in another window.)

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the backbone of the protein will show the constituent residues in the chain.

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space-filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see the atoms in the protein.

Now, let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

[[Eleanor_Crabb/The_four_tiers_of_protein_structure|Next page - The four tiers of protein structure]]

S347/The four tiers of protein structure

2009-10-20T15:29:57Z

User:Eleanor Crabb/Sandbox 2

2009-10-20T15:18:04Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 2

2009-10-20T15:15:44Z

Eleanor Crabb:

== '''The four tiers of protein structure''' ==

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/4'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/4'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/1'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Sandbox 2

2009-10-20T15:13:32Z

Eleanor Crabb:

== '''The four tiers of protein structure''' ==

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/3'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/3'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/1'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Sandbox 2

2009-10-20T15:11:04Z

Eleanor Crabb:

== '''The four tiers of protein structure''' ==

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/2'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/3'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/1'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Sandbox 2

2009-10-20T15:06:21Z

Eleanor Crabb:

== '''The four tiers of protein structure''' ==

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/2'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/2'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/1'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Sandbox 2

2009-10-20T15:05:59Z

Eleanor Crabb:

'''The four tiers of protein structure'''

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/2'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the hydrogen atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The hydrogen bonding in the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/2'> beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein, as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/1'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Sandbox 2

2009-10-20T14:59:52Z

Eleanor Crabb:

'''The four tiers of protein structure'''

We will use the structure of the zinc-containing enzyme '''1z3a''' to identify the four tiers of protein structure. <applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />

The '''primary structure''' of a protein is simply the arrangement of amino acid residues within the chains. This can be emphasized by colouring just the chains according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene> (in this example we will use just Chain A to illustrate this). Hover your cursor over the molecule to identify some of the different residues present.

The protein can also be coloured according to '''secondary structure'''. The elements of <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> in this protein are the alpha-helices shown in pink and the beta-sheets in yellow. The interconnecting loops and any other features are shown in white. Rotate the molecule to look at these elements in more detail. If we now consider just one <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_ahelix_hbonds/1'>alpha-helix</scene> we can see how this secondary structure is held together by hydrogen bonds - shown here as dashed lines. Remember that the H atoms are not displayed in the protein so the lines join the atoms that are hydrogen bonded together (without the bonded hydrogen atom). The <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_bsheet_hydrogenbnds/1'>hydrogen bonding in the beta-sheet</scene> can also be illustrated.

As an enzyme, this protein is an example of a globular protein as we can see when consider the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_spacefilled/1'>space-filled representation</scene> of the entire protein, both chains A and B. This the '''tertiary structure''' of the protein.

Finally, the '''quaternary structure''' refers to the number of subunits in the protein. In this particular example, the biological molecule is the same as the shown <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chainaandb/1'>asymmetric unit of 1z3a</scene> shown here and so there are two. The protein is thus a dimer.

User:Eleanor Crabb/Sandbox 2

2009-10-08T22:48:27Z

Eleanor Crabb:

Protein structure

Returning now to both chains in the structure '''1z3a''' we will use this to identify the four tiers of protein structure.<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' /><scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina/1'> the amino acid residue</scene>
The '''primary structure''' is simply the arrangement of amino acid residues with in the chain. This can be emphasized by colouring Chain A according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene>. Hover your cursor over the molecule to identify some of the different residues present in the protein.

The protein can also be coloured according to the '''secondary structure'''. The <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene>here are the alpha-helices shown in pink, beta-sheets in yellow, with the interconnecting loops in white. Rotate the molecule to look at these features in more detail. If we now consider just the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_hbonds/1'>backbone with hydrogen bonds</scene> we can see how this secondary structure is held together by hydrogen bonds.

As an enzyme, this protein is an example of a globular protein as we can see when consider the space-filled representation of the entire protein, both chains A and B. This the tertiary structure of the protein.

Finally, the quaternary structure here refers . In this particular example

User:Eleanor Crabb/Sandbox 2

2009-10-08T22:29:51Z

Eleanor Crabb:

Protein structure

Returning now to both chains in the structure 1z3a we will use this to identify the four tiers of protein structure.<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' /><scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina/1'> the amino acid residue</scene>
The '''primary structure''' is simply the arrangement of amino acid residues with in the chain. This can be emphasized by colouring Chain A according to <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_amino/1'>residue</scene>. Hover your cursor over the molecule to identify some of the different residues present in the protein.

The protein can also be coloured according to the '''secondary structure'''. In the <scene name='User:Eleanor_Crabb/Sandbox_2/1z3a_chaina_secondarystructure/1'>secondary structure</scene> a-helices are shown in pink and <math>b</math>-sheets in yellow. Rotate the molecule to look at these features in more detail.

User:Eleanor Crabb/Sandbox 2

2009-10-08T22:18:42Z

Eleanor Crabb:

Protein structure

Returning now to both chains in the structure 1z3a we will use this to identify the four tiers of protein structure.
The primary structure is simply the arrangement of amino acid residues with in the chain. This can be emphasized by colouring Chain A according to residue.

User:Eleanor Crabb/Sandbox 2

2009-10-08T22:13:46Z

Eleanor Crabb: New page: Protein structure In this example

Protein structure

In this example

User:Eleanor Crabb/Sandbox 1

2009-10-08T22:07:19Z

Eleanor Crabb:

<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule.

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, if you hover your cursor over the grey atom you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the grey backbone of the protein will show the constituent residues in the chain.

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see more clearly the atoms in the protein.

Now, let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene> Hover your cursor over the molecule to identify some of the different residues in the chain.

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

User:Eleanor Crabb/Sandbox 1

2009-10-08T21:59:29Z

Eleanor Crabb:

<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>

Let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

User:Eleanor Crabb/Sandbox 1

2009-10-08T21:58:18Z

Eleanor Crabb:

<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.jpg]]

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>

Let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

File:Elementbox.JPG

2009-10-08T21:56:50Z

Eleanor Crabb: Label for Zn in Chain A 1z5a

Label for Zn in Chain A 1z5a

User:Eleanor Crabb/Sandbox 1

2009-10-08T21:52:24Z

Eleanor Crabb:

<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see [[Image:Example.jpg]]

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>

Let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

User:Eleanor Crabb/Sandbox 1

2009-10-08T21:49:18Z

Eleanor Crabb:

<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see ZN 301, Chain A Element Zn

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>

Let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

User:Eleanor Crabb/Sandbox 1

2009-10-08T21:46:33Z

Eleanor Crabb:

<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example,

This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>

Let us simplify things further by looking at just a
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

User:Eleanor Crabb/Sandbox 1

2009-09-29T11:27:14Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T22:02:39Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T21:58:27Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T21:54:41Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T21:47:04Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T20:33:48Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T20:23:15Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T19:52:14Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T19:35:59Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T19:13:29Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T19:07:05Z

Eleanor Crabb:

User:Eleanor Crabb/Sandbox 1

2009-09-18T18:56:20Z

Eleanor Crabb: New page: <applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package ...

User:Eleanor Crabb

2009-09-18T18:32:09Z

Eleanor Crabb:

Dr Eleanor Crabb
Lecturer in Chemistry
Department of Chemistry and Analytical Sciences
The Open University
Walton Hall
Milton Keynes
MK7 6AA
UK

*[[User:Eleanor Crabb/Sandbox 1]]