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, (b) Name of the molecule, (c) experimental method for structure determination and (d) Resolution of the structure.
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 .
4. Give the Class, Fold, Superfamily and Family of this protein in Structural Classification of Proteins (SCOP).
5. (a) Show Ramachandran plot for this PDB file. (b) How many residues are in the most favoured regions of Ramachandran plot?

1. 由於在PDB內沒有收錄"MLH1"的結構資料，所以我們找與此基因相似的來做結構上的分析。進入PDB中的"Protein Data Bank"，是其主要的搜索引擎。鍵入"mutL"後按下"Find a structure"，可以找到三個附合條件，不過我們不要複合物(complex)所以選擇1BKN。 (a)ID number:1BKN (b)Name:N-Terminal 40Kd Fragment Of E. Coli DNA Mismatch Repair Protein Mutl (c)Exp Method:X-ray Diffraction (d)Resolution:2.90埃 網站資料 Link

2. 在詳細資料的左方有"View Structure"可看其結構。用最下方的"Custom Size Images"來調整自己想要的大小。 1BKN

3. 在詳細資料的左方有"Download/Display File"可顯示結構方面的資訊。選擇"complete with coordinates"的完整資料，型式可自行選擇。(a)2chains (b)A有11個螺旋，B有10個螺旋。 (c)第六螺旋的第一個胺基酸為Threonine，最後一個為Alanine。 網站資料 Link

4. 從"Structure Neighbors"中可找到SCOP，關於1BKN的分類有兩種。 其之一：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. 網站資料 Link 其之二：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. 網站資料 Link

5. 在"Other source"中找到"Summary of PDB Structure"，直接點選右邊的"1bkn"，可得到此蛋白質的一些資料，其中點選中間有個四方形的圖示，再找到上面的"Ramachandran plot"便能顯示作圖。胺基酸最密集的區域[A,B,L]有379個胺基酸。 ramach-1BKN 網站資料 Link