User:Eleanor Crabb/Sandbox 1

From Proteopedia

proteopedia linkproteopedia link

Revision as of 21:58, 18 September 2009 (edit) Eleanor Crabb (Talk | contribs) ← Previous diff		Revision as of 22:02, 18 September 2009 (edit) (undo) Eleanor Crabb (Talk | contribs) Next diff →
Line 6:		Line 6:
	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 that the H atoms are not shown):		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 that the H atoms are not shown):
-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/1'>space- filled</scene> - this gives an indication of the size and shape of the protein	+	*<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>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>
Line 14:		Line 14:
	Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:		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>	+	*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_nc/1'>NC</scene>
	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</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_site/1'>residues within 30 nm</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>

---

Revision as of 22:02, 18 September 2009

spinqualitylabelsall models Insert caption here Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 Protein Data Bank to visualise proteins.

The interactive image on the right shows the protein with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom 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 , chain A. To see this click on the link in green.

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 that the H atoms are not shown):

• - this gives an indication of the size and shape of the protein

Let us simplify things further by looking at just a 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 or the alone.

Returning now to . This can be coloured according to:

• the arrangement of the

Finally, focussing now on the zinc atom