User:Eric Martz/Cavities tests: Difference between revisions
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[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol] | [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol] | ||
When the [[PDB]] is searched with the dnaC sequence, the closest hit is 39% identity with residues 9-63 of chain A of replication factor C (2CHG), which align with 72-124 of dnaC. When the above homology model of dnaC (made with template 2QGZ) is structurally aligned with residues 9-63 of 2CHG<ref>Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.</ref>, 43 alpha carbons (out of 54) aligned with RMS deviation 2.3 Å. Residues 21-63 of 2CHG aligned with residues 80-124 of the dnaC homology model. This result adds some confidence to the homology model, since the structural alignment of 2CHG:A21-63 occurred in the same range as the sequence alignment (which was 72-124 in dnaC). | |||
==Crystal Structure of DnaC== | ==Crystal Structure of DnaC== | ||