Structure of E. coli DnaC helicase loader: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 22: | Line 22: | ||
scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8' /> | scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8' /> | ||
The homology model (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8'>restore initial scene</scene>) represents 75% of the full length ''E. coli'' DnaC sequence, omitting 54 N-terminal residues, and 8 C-terminal residues. Several surface loops in the model (shown translucent white) have high uncertainty, since these are missing in the template ([[#Homology Model Construction|see below]]). Note that the homology model is somewhat unreliable about which residues are actually on the surface vs. largely buried, and hence the conclusions below are tentative. | The homology model (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8'>restore initial scene</scene>) represents 75% of the full length ''E. coli'' DnaC sequence, omitting 54 N-terminal residues, and 8 C-terminal residues. Note that the N-terminal 76 residues are predicted to be intrinsically unfolded (see [[#Intrinsically Unstructured N-Terminus|above]]). Several surface loops in the model (shown translucent white) have high uncertainty, since these are missing in the template ([[#Homology Model Construction|see below]]). Note that the homology model is somewhat unreliable about which residues are actually on the surface vs. largely buried, and hence the conclusions below are tentative. | ||
{{Template:ColorKey_Amino2CarboxyRainbow}} | {{Template:ColorKey_Amino2CarboxyRainbow}} | ||
| Line 45: | Line 45: | ||
*The <scene name='User:Eric_Martz/Sandbox_6/3ecc/1'>same two conserved surface patches</scene><ref>[http://consurf.tau.ac.il/results/1230090558/output.html ConSurf result] using 50 sequences from Uniprot, with an average pairwise distance in the multiple sequence alignment of 1.6.</ref> are observed on the 2.7 Å crystal structure of DnaC from ''Aquifex aeolicus'' ([[3ecc]]), where the '''larger conserved patch is the binding site for ATP/ADP'''. | *The <scene name='User:Eric_Martz/Sandbox_6/3ecc/1'>same two conserved surface patches</scene><ref>[http://consurf.tau.ac.il/results/1230090558/output.html ConSurf result] using 50 sequences from Uniprot, with an average pairwise distance in the multiple sequence alignment of 1.6.</ref> are observed on the 2.7 Å crystal structure of DnaC from ''Aquifex aeolicus'' ([[3ecc]]), where the '''larger conserved patch is the binding site for ATP/ADP'''. | ||
==Homology Model Construction== | ==Homology Model Construction== | ||