1. 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, (b) Name of the molecule, (c) experimental method for structure determination and (d) Resolution of the structure.

ANS:
(a)ID number:1AZO
(b)name of the molecule:DNA Mismatch Repair Protein Muth From E. Coli
(c)experimental method for structure determination:X-ray Diffraction
(d)Resolution of the structure [A]: 1.70

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

3. Give the structural informations of this PDB file (a) number of protein chains, (b) number of helix in one protein chain, (c) the first and last residues in the helix 6 .

(a) number of protein chains:Null
(b) number of helix in one protein chain:9
(c) the first and last residues in the helix 6 : LEU &GLN

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

1. Root: scop
2. Class: Alpha and beta proteins (a/b)
   Mainly parallel beta sheets (beta-alpha-beta units)
3. Fold: Restriction endonuclease-like
   core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
4. Superfamily: Restriction endonuclease-like
5. Family: DNA mismatch repair protein MutH from

Protein: DNA mismatch repair protein MutH from

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

(b)166