5002 Protein Set - Page 3

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3) Three-dimensional coordinates and their treatment Those coordinates of proteins whose structures are already known are registered in the Protein Data Bank (PDB). Here, modeling is explaind according to the adove coordinates. Classify the PDB coordinates into groups X-Y, X-Z, Y-Z and draw your map by plotting them. You can easily find how to connect them and to make a map, if you plot the amino acids one by one. It is troublesome work to draw a map manually, and you can use a computer to do the work. Draw a chain of some 10 to 20 amino acids in one sheet of A3(*) size paper. You need to draw 2 maps, one showing main chains only and the other showing main chains including side chains. (*)A3 size paper: = Approx 42X30 cm / Approx 17"X11" Note: Same procedures as above will be effective for a protein of uncertain 3-D coordinates.

Fig. 3 Fig. 4

Coordinates of Myoglobin

Myoglobin PDB data No Residue Atom X Y Z 1 VAL 1 N 1.000 15.700 29.000 2 CA 1.400 14.800 27.500 3 C 2.500 13.800 28.200 4 O 2.500 12.600 27.900 5 CB 1.900 15.700 26.600 6 CG1 2.100 14.800 25.400 7 CG2 0.800 16.700 26.300 2 LEU 1 N 3.900 13.900 28.400 2 CA 4.700 13.000 29.200 3 C 4.300 12.800 30.700 4 O 4.100 13.900 31.300 5 CB 6.300 13.400 29.200 6 CG 6.800 13.100 27.800 7 CD1 6.700 14.400 26.900 8 CD2 8.300 12.700 27.900 3 SER 1 N 4.400 11.500 31.100 2 CA 4.100 11.300 32.600 3 C 5.300 11.800 33.400 4 O 6.400 12.000 32.900 5 CB 3.900 9.800 32.900 6 OG 5.000 9.000 27.900

Myoglobin PDB data No Residue Atom X Y Z 4 GLU 1 N 5.100 11.900 34.700 2 CA 6.200 12.500 35.600 3 C 7.300 11.400 35.600 4 O 8.500 11.700 35.600 5 CB 5.600 12.800 37.000 6 CG 6.300 14.000 37.800 7 CD 5.900 15.400 37.300 8 OE1 4.700 15.800 37.200 9 OE2 6.900 16.000 37.000 5 GLY 1 N 6.800 10.200 35.600 2 CA 7.700 9.100 35.300 3 C 8.700 9.200 34.100 4 O 9.900 9.000 34.300 6 GLU 1 N 8.200 9.700 33.000 2 CA 9.100 9.600 31.700 3 C 9.900 10.900 31.800 4 O 11.000 11.000 31.200 5 CB 8.200 9.600 30.500 6 OG 7.400 8.300 30.200 7 CD 6.200 8.400 29.100 8 OE1 6.000 7.500 28.300 9 OE2 5.700 9.500 29.200

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