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| ==Introduction to proteins==
| | #REDIRECT [[User:James D Watson/Proteins Intro]] |
| This will be the start of an attempt to create a topic based page that could be used in teaching. I will spend more time editing it asap.
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| <scene name='James_D_Watson/Proteins_Intro/Ligand_binding_site_ras/1'>Click to see walker motif</scene>
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| {{STRUCTURE_5p21 | PDB=5p21 | SCENE= }}
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| ==Structural superposition==
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| The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 coloured red) with Gdp-bound human rab21 gtpase (PDB entry 1z0i - coloured blue), the structural superposition was made using the MSDfold(SSM)[http://www.ebi.ac.uk/msd-srv/ssm/ 1] server at the EBI[http://www.ebi.ac.uk 2]. Note that the global fold of these two proteins is almost identical yet their sequence identity is only 29.6% (as determined using FASTA). The viewer below right shows the p-loops of both structures superposed. The ligands bound superpose particularly well and comparison of the two p-loops loops show significant structural similarity but also highlights the sequence differences between the two proteins.
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| <applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
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| <applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />
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