Sandbox6 Eric Martz

Please do not edit this page. Eric Martz, February 2011.

Homology Model for 83-341Homology Model for 83-341

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

• Homology model of 83-341 on template chain A of 3e4c, 52% sequence identity (). Confidence in this model is high because of the 52% sequence identity and sequence alignment with only one 10-residue gap.

Amino Terminus

Carboxy Terminus

• .
• The seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model.

Anionic (-) / Cationic (+)

• The inner face of 95-140 is . Bear in mind that sidechain positions are incorrect in a homology model. . The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the .

• The inner face of 95-140 is , even based upon a multiple sequence alignment that includes mostly types other than 12 .

• When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a , namely Asn130, Val135, Val136, Glu139, Asn140. .

• The homology model can be downloaded from homology-model-83-341.

Homology Model for 2-88Homology Model for 2-88

• Swiss-Model produced a using chain A of 1dgn as template. Confidence in this model is low because the sequence alignment had only 19% identity.
• This model shows a , with a large region containing only negative charges.

Anionic (-) / Cationic (+)

• I am still working on the analysis of evolutionary conservation in this model. (I ran into some problem with the ConSurf server and am communicating with the group in Tel-Aviv.)
• This model can be downloaded from model-2-88.