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.

answer: (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 deterimination= X-ray Diffraction

             (d) Resolution of the structure= 2.90 A

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

answer:

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 .

answer: (link)

             (a) number of protein chains= 2 (A,B)

             (b) number of helix in one protein chain= A chain : 11 helix ; B chain : 10 helix

             (c) the first and last residues in the helix 6= first: Thr ; last= Ala

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

answer: There are two results :

(1)Root: scop
    Class: Alpha and beta proteins (a+b)
    Mainly antiparallel beta sheets (segregated alpha and beta regions)
    Fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
    8-stranded mixed beta-sheet; 2 layers: alpha/beta
    Superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
    Family: DNA gyrase/MutL, N-terminal domain
    Protein: DNA mismatch repair protein MutL
    Species: Escherichia coli
    (link)

(2)Root: scop
    Class: Alpha and beta proteins (a+b)
    Mainly antiparallel beta sheets (segregated alpha and beta regions)
    Fold: Ribosomal protein S5 domain 2-like
    core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
    Superfamily: Ribosomal protein S5 domain 2-like
    Family: DNA gyrase/MutL, second domain
    Protein: DNA mismatch repair protein MutL
    Species: Escherichia coli
    (link)

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

answer:

(a) (link)

(b) 379