Sandbox1234
From Proteopedia
(Difference between revisions)
(New page: '''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!''' ==Glucokinase== The shown representation is a DNA:RAN hybrid duplex...) |
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'''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!''' | '''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!''' | ||
| - | == | + | ===DNA:RNA interactions==={{STRUCTURE_124d| PDB=124d | SCENE= }} |
The shown representation is a DNA:RAN hybrid duplex. This is the | The shown representation is a DNA:RAN hybrid duplex. This is the | ||
| - | <scene name='Sandbox1234/Dna/1'>DNA</scene> in orange and this is the <scene name='Sandbox1234/Rna/1'>RNA</scene> in green. We can choose to see the base pairs, which show very neatly. First, the G-C pairs: <scene name='Sandbox1234/Dg-c/1'>dG-C</scene> are in blue and dC-G are in yellow. | + | <scene name='Sandbox1234/Dna/1'>DNA</scene> in orange and this is the <scene name='Sandbox1234/Rna/1'>RNA</scene> in green. We can choose to see the base pairs, which show very neatly. First, the G-C pairs: <scene name='Sandbox1234/Dg-c/1'>dG-C</scene> are in blue and dC-G are in yellow. Similarly, we can see the dA-U in red and the dT-A in purple (note that the RNA has U nucleotides instead of T). Furthermore, we can also see the purine and pyrimidine for a more general view of the bases. Because this is the B form of DNA:RNA interaction, all hydrogen bonds between the bases are through the Watson Crick faces. If we choose to see the ions, as we'd expect, the whole complex shines. |
| - | ===Structure==={{STRUCTURE_1v4s| PDB=1v4s | SCENE= }} | ||
| - | The glucokinase has 18 <scene name='Sandbox22/Alpha_helices/1'>alpha helices</scene> (unless we counted wrong), 13 <scene name='Sandbox22/Beta_sheets/5'>beta sheets</scene> (this one is for sure), and 3 <scene name='Sandbox22/Ligands/1'>ligands</scene>: a <scene name='Sandbox22/Sodium_ion/1'>sodium ion</scene>, <scene name='Sandbox22/Glc/1'>T2 amino-4-fluoro-5-[(1-methyl-1h-amidazol-2-yl)sulfanyl]-n-(1,3-thiazol-2-yl)benzamide</scene> | ||
| - | amide or MRK in short, and last a sugar (alpha-d-glucose) or simply GLC. | ||
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| - | Purple denotes all the <scene name='Sandbox22/Amphilphillic/1'>polar</scene> sections of the protein: the hydrophillic areas that dominate the outer surface which comes in contact with aqueous environments. In this view we can see very neatly how the beta sheets alternate in polarity in a 'zigzag manner, and how the alpha helices are roughly 2-3 polar (while the inner protein is obviously hydrophobic). The | ||
| - | <scene name='Sandbox22/Spacefill/1'>spacefill representation</scene>, in particular, shows how the surface is dominantly hydrophillic. | ||
===Reference=== | ===Reference=== | ||
| - | http://www. | + | http://www.rcsb.org/pdb/explore.do?structureId=124d |
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Revision as of 13:55, 23 May 2009
This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!
DNA:RNA interactions
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| 124d, 1 NMR models () | |||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The shown representation is a DNA:RAN hybrid duplex. This is the
in orange and this is the in green. We can choose to see the base pairs, which show very neatly. First, the G-C pairs: are in blue and dC-G are in yellow. Similarly, we can see the dA-U in red and the dT-A in purple (note that the RNA has U nucleotides instead of T). Furthermore, we can also see the purine and pyrimidine for a more general view of the bases. Because this is the B form of DNA:RNA interaction, all hydrogen bonds between the bases are through the Watson Crick faces. If we choose to see the ions, as we'd expect, the whole complex shines.
