Journal:MicroPubl Biol:000574
From Proteopedia
(Difference between revisions)
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*Very high (pLDDT > 90) <span class="text-blue">'''blue'''</span> | *Very high (pLDDT > 90) <span class="text-blue">'''blue'''</span> | ||
| - | The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. <scene name='91/919077/Cv/5'>A structural overlay</scene> of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB [[6j9c]]), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated <scene name='91/919077/Cv/6'>positively charged residues surrounding the DNA-binding site</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) that could interact with the negatively charged DNA backbone and mapping of the level of conservation for each residue showed that the residues within this site were all highly conserved among homologs of this protein, as determined by the ConSurf program. | + | The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. <scene name='91/919077/Cv/5'>A structural overlay</scene> of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB [[6j9c]]), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated <scene name='91/919077/Cv/6'>positively charged residues surrounding the DNA-binding site</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) that could interact with the negatively charged DNA backbone and mapping of the level of conservation for each residue showed that the residues within this site were all highly conserved among homologs of this protein, as determined by the ConSurf program. |
<b>References</b><br> | <b>References</b><br> | ||
Revision as of 11:06, 11 August 2022
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This page complements a publication in scientific journals and is one of the Proteopedia's Interactive 3D Complement pages. For aditional details please see I3DC.
