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.

(a) 1B62

(b) Mutl Complexed With ADP

(c) X-ray Diffraction

(d) 2.10 A


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) 2-A,B

(b)15

(c) first one-Glu97 , last one-Val105


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

(1)

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

(2)

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


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

(a)

(b)257