Homework 7

Protein Structure Database -PDB-.

- To do Protein Structure data search
- To understand protein structure data file
- Deadline - 12/11/2001

  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 = 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).
    Ans.

  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 .
    Ans. (a) number of protein chains = 2(1BKN:A ; 1BKN:B) , (b) number of helix in one protein chain = 1BKN:A = 11 ; 1BKN:B = 10 , (c) the first and last residues in the helix 6 = Thr Ala
  4. Give the Class, Fold, Superfamily and Family of this protein in Structural Classification of Proteins (SCOP).
    Ans. (a) 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 (b) Class = Alpha and beta proteins (a+b) ; Fold = Ribosomal protein S5 domain 2-like ; Superfamily = Ribosomal protein S5 domain 2-like ; Family = DNA gyrase/MutL, second domain
  5. (a) Show Ramachandran plot for this PDB file. (b) How many residues are in the most favoured regions of Ramachandran plot?
    Ans. (a)

    (b) 379