JMol applet (HTML5)
PDB ID: 4NK1
PHOSPHATE-BOUND HELL'S GATE GLOBIN IV
RESULTS | |||
| 1. | The biggest hydrophobic core is #2 (pink spacefill structure), it contains 735 atoms, that is about 25% of all atoms in protein (2967). It is easy to see that protein structure is not fully covered with core#2, all open hydrophobic areas are (probably) hidden by other molecules atoms.I may suggest that they are used in different molecules interactions. | ||
| 2. | For this task was chosen PHE125 (chain A). Starting from 4 Angstroms (there was no surrounding on 1A level and 2-3 wasn't good enough), the chosen amino acid is almost fully covered by surrounding residues. The average distance between 2 non-covalent atoms is about 3.33 Angstroms which is not long enough for such molecule as water to fit in because even if are speaking about the shortest distance, when we have 2 atoms of oxygen, we will get 5.6 Angstroms as a result (1,4A + 1,4*2(diameter of one H2O molecule) + 1,4)[1], which is longer than the average (and even longer than the most possible) distance. | 3. | For the third task i have got DNA polymerase eta which is actually quite interesting. It is a member of DNA repair process (TLS [2]). DNA polymerase eta is encoded by POLH gene, loss of which causes xeroderma pigmentosum (inability to repair damage caused by UV light)[3]. |
1. The Elements, J. Emsley, 1993.
2.Wikipedia. Translesion synthesis
3.Wikipedia. Xeroderma pigmentosum