James D Watson/Proteins Intro
From Proteopedia
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==Structural superposition== | ==Structural superposition== | ||
| - | The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 <nowiki>-</nowiki> coloured | + | The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 <nowiki>-</nowiki> coloured orange) with Gdp-bound human rab21 gtpase (PDB entry 1z0i <nowiki>-</nowiki> 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. |
<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' /> | <applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' /> | ||
<applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' /> | <applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' /> | ||
Revision as of 10:37, 5 June 2008
Introduction to proteins
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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| 5p21, resolution 1.35Å () | |||||||||
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| Ligands: | , | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Structural superposition
The viewer below left shows the structural superposition of the triphosphate conformation of H-ras p21 (PDB entry 5p21 - coloured orange) with Gdp-bound human rab21 gtpase (PDB entry 1z0i - coloured blue), the structural superposition was made using the MSDfold(SSM)1 server at the EBI2. 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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