Protein Structure Database -PDB-
- To do Protein Structure data search
- To understand protein structure data file
 

 

1. Search human Mlh1 or its homologous proteins in Protein Data Bank (PDB) database. You just need to search for protein structure, do not find complex structure. Give its

(a) ID number : 1BKN

(b) Name of the molecule :

Crystal Structure Of An N-Terminal 40Kd Fragment Of E. Coli DNA Mismatch Repair Protein Mutl

(c) experimental method for structure determination : X-ray Diffraction

(d) Resolution of the structure : 2.90
 

2. Show its structure in ribbons form (400x400).
 

3. Give the structural informations of this PDB file

(a) number of protein chains : 2

(b) number of helix in one protein chain : 11

(c) the first and last residues in the helix 6 : Thr 166 - Ala 181
 

4. Give the Class, Fold, Superfamily and Family of this protein in Structural Classification of Proteins (SCOP).

Class: Alpha and beta proteins (a+b)

Fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase

Superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase

Family: DNA gyrase/MutL, N-terminal domain

link

 

5. (a) Show Ramachandran plot for this PDB file. (b) How many residues are in the most favoured regions of Ramachandran plot?


379 residues are in the most favoured regions of Ramachandran plot.