Sandbox Reserved 791
From Proteopedia
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<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' /> | <Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' /> | ||
| - | This is a tetrameric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl_CoA_synthetase</scene> with the known binding ligands present in the protein crystallization. | + | This is a tetrameric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl_CoA_synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted |
To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown. | To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown. | ||
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We can see the <scene name='56/563203/Hydrophilics/1'>hydrophilic residues in ribbon form</scene> here while the <scene name='56/563203/Hydrophobics/2'>hydrophobic residues in ribbon form</scene> are visible as well. | We can see the <scene name='56/563203/Hydrophilics/1'>hydrophilic residues in ribbon form</scene> here while the <scene name='56/563203/Hydrophobics/2'>hydrophobic residues in ribbon form</scene> are visible as well. | ||
| - | We can get a clearer picture of the <scene name='56/563203/Hydrophobics_transparency_2/1'>hydrophobic</scene> chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to obtain the <scene name='56/563203/Hydrophilic_transparency_1/1'>hydrophilic chains</scene>, which are shown in light brown. | + | We can get a clearer picture of the <scene name='56/563203/Hydrophobics_transparency_2/1'>hydrophobic</scene> chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to obtain the <scene name='56/563203/Hydrophilic_transparency_1/1'>hydrophilic chains</scene>, which are shown in light brown. We can see that the hydrophobic residues are mostly located on the interior of the protein while the hydrophilic residues are mostly interacting with the protein's exterior. |
Water is often crystallized with the protein, and we can show portions of | Water is often crystallized with the protein, and we can show portions of | ||
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We can also see the same effects for the other chains: | We can also see the same effects for the other chains: | ||
<scene name='56/563203/Water_interactions_chain_b/1'>Chain B</scene>'s water interactions (in red) are depicted and its <scene name='56/563203/Waterandsolv_inter_chain_b/1'>ligand</scene> sites are also observed (CoA (fuchsia), sulfate (purple)). | <scene name='56/563203/Water_interactions_chain_b/1'>Chain B</scene>'s water interactions (in red) are depicted and its <scene name='56/563203/Waterandsolv_inter_chain_b/1'>ligand</scene> sites are also observed (CoA (fuchsia), sulfate (purple)). | ||
| - | <scene name='56/563203/Water_interactions_chain_c/1'>Chain | + | <scene name='56/563203/Water_interactions_chain_c/1'>Chain D</scene>'s water (in red) are depicted. Its <scene name='56/563203/Waterandsolv_inter_chain_d/1'>ligand </scene> binding sites are also observed (CoA (fuchsia), glycerol (indigo). |
| + | <scene name='56/563203/Water_interactions_chain_e/1'>Chain E</scene>'s water interactions (in red) are depicted and its | ||
| + | <scene name='56/563203/Waterandsolv_inter_chain_e/1'>ligand</scene> binding sites are also observed (CoA (fuchsia), sulfate (purple). | ||
Revision as of 19:43, 16 October 2013
| This Sandbox is Reserved from Oct 10, 2013, through May 20, 2014 for use in the course "CHEM 410 Biochemistry 1 and 2" taught by Hanna Tims at the Messiah College. This reservation includes Sandbox Reserved 780 through Sandbox Reserved 807. |
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This is a tetrameric protein with the known binding ligands present in the protein crystallization. The four chains depicted To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the model, as shown.
This depicts the hydrogen bonding present in the backbone for the protein.
The are represented here
Here's some for the beta sheet.
Here are the
We can see the here while the are visible as well.
We can get a clearer picture of the chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to obtain the , which are shown in light brown. We can see that the hydrophobic residues are mostly located on the interior of the protein while the hydrophilic residues are mostly interacting with the protein's exterior.
Water is often crystallized with the protein, and we can show portions of where water molecules (light blue) interacts with the chain. We can also analyze the presence of ligand molecules at sites, where CoA (fuchsia), phosphate (green) and glycerol (indigo) bind.
We can also see the same effects for the other chains: 's water interactions (in red) are depicted and its sites are also observed (CoA (fuchsia), sulfate (purple)). 's water (in red) are depicted. Its binding sites are also observed (CoA (fuchsia), glycerol (indigo). 's water interactions (in red) are depicted and its binding sites are also observed (CoA (fuchsia), sulfate (purple).
