RasMol-скрипт, демонстрирующий область контакта
глюкозамин-6-фосфата с глюкозамин-6-фосфатсинтазой

    Листинг 1. RasMol-скрипт, демонстрирующий область контакта глюкозамин-6-фосфата с глюкозамин-6-фосфатсинтазой и иллюстрирующий генноинженерный эксперимент

BACKGROUND WHITE
SET FONTSIZE 10
SET FONTSTROKE 1
COLOR CPK
RESTRICT NONE

DEFINE CONT_PHOSPH SER303, SER347, GLN348, SER349, THR352
DEFINE PHOSPH_ATOMS SER303.OG, SER347.OG, GLN348.N, SER349.N, SER349.OG, THR352.OG1, HOH8, HOH9
ECHO The sets CONT_PHOSPH and PHOSPH_ATOMS are defined
ECHO The set CONT_PHOSPH contains residues contacting to phosphate group
ECHO The set PHOSPH_ATOMS contains atoms contacting to phosphate group
ECHO
DEFINE CONT_O3 THR302, SER401, GLU488, LYS603
DEFINE O3_ATOMS THR302.OG1, SER401.OG;B, GLU488.OE2, LYS603.NZ, HOH3, HOH99
ECHO The sets CONT_O3 and O3_ATOMS are defined
ECHO The set CONT_O3 contains residues contacting to 3-OH group
ECHO The set O3_ATOMS contains atoms contacting to 3-OH group
ECHO
DEFINE CONT_N2 VAL399, GLU488, ALA602
DEFINE N2_ATOMS VAL399.O, GLU488.OE2, ALA602.O, HOH11
ECHO The sets CONT_N2 and N2_ATOMS are defined
ECHO The set CONT_N2 contains residues contacting to 2-NH2 group
ECHO The set N2_ATOMS contains atoms contacting to 2-NH2 group
ECHO
DEFINE CONT_O14 THR302, ALA602
DEFINE O14_ATOMS THR302.N, ALA602.N, HOH18
ECHO The sets CONT_O14 and O14_ATOMS are defined
ECHO The set CONT_O14 contains residues contacting to 1-OH and 4-OH groups
ECHO The set O14_ATOMS contains atoms contacting to 1-OH and 4-OH groups
ECHO
DEFINE CONT_GLP CONT_PHOSPH, CONT_O3, CONT_N2, THR302, ALA602
DEFINE GLP_ATOMS PHOSPH_ATOMS, O3_ATOMS, N2_ATOMS, THR302.N, ALA602.N, HOH18
ECHO The sets CONT_GLP and GLP_ATOMS are defined
DEFINE AA1 SER347
DEFINE AA1_V2 GLU488
DEFINE AA2 SER349
DEFINE AA2_V2 ALA602
ECHO
ECHO The sets AA1 and AA1_V2 are defined
ECHO AA1 is aminoacid to be replaced by tryptophan
ECHO AA1_V2 is aminoacid to be replaced by methionine
ECHO
ECHO The sets AA2 and AA2_V2 are defined
ECHO AA2 is aminoacid to be replaced by threonine
ECHO AA2_V2 is aminoacid to be replaced by glycine
ECHO

ECHO Glucosamine 6-phosphate contacts are under consideration
ZOOM 400
RESTRICT GLP
LABELS OFF
BOND 475 2842 +
BOND 833 2842 +
BOND 842 2841 +
BOND 847 2841 +
BOND 832 2840 +
BOND 866 2840 +
BOND 866 2897 +
BOND 2896 2842 +
BOND 2896 2836 +
BOND 2897 2837 +
BOND 2897 2838 +
SELECT GLP.O4, GLP.O5, GLP.O6, GLP.O1P, GLP.O2P, GLP.O3P
LABEL %n%a
SELECT CONT_PHOSPH
WIREFRAME 30
COLOR CPK
SELECT PHOSPH_ATOMS
CPK 60
LABEL %n%r%a
SELECT WATER
COLOR BLUE
ECHO
ECHO Phosphate group contacts are displayed
ECHO Press any key to display 3-OH group contacts

PAUSE
RESTRICT GLP
CPK OFF
LABELS OFF
BOND 468 2891 +
BOND 1892 2891 +
BOND 2891 2835 +
BOND 1211 2987 +
BOND 2788 2987 +
BOND 2987 2835 +
SELECT GLP.O3
CPK 140
LABEL %n%a
SELECT CONT_O3
WIREFRAME 50
COLOR CPK
SELECT O3_ATOMS
CPK 100
LABEL %n%r%a
SELECT WATER
COLOR BLUE
ECHO
ECHO 3-OH group contacts are displayed
ECHO Press any key to display 2-NH2 group contacts

PAUSE
RESTRICT GLP
CPK OFF
LABELS OFF
BOND 1892 2899 +
BOND 2899 2834 +
BOND 1196 2834 +
BOND 2778 2834 +
SELECT GLP.N2
CPK 140
LABEL %n%a
SELECT CONT_N2
WIREFRAME 50
COLOR CPK
SELECT N2_ATOMS
CPK 100
LABEL %n%r%a
SELECT WATER
COLOR BLUE
ECHO
ECHO 2-NH2 group contacts are displayed
ECHO Press any key to display 1-OH and 4-OH groups contacts

PAUSE
RESTRICT GLP
CPK OFF
LABELS OFF
BOND 463 2836 +
BOND 2775 2906 +
BOND 2906 2833 +
SELECT GLP.O1, GLP.O4
CPK 140
LABEL %n%a
SELECT CONT_O14
WIREFRAME 50
COLOR CPK
SELECT O14_ATOMS
CPK 100
LABEL %n%r%a
SELECT WATER
COLOR BLUE
ECHO
ECHO 1-OH and 4-OH groups contacts are displayed
ECHO Press any key to display all glucosamine 6-phosphate contacts

PAUSE
RESTRICT GLP
SPACEFILL
LABELS OFF
SELECT GLP.P
LABEL Glucosamine-6-phosphate
SELECT CONT_GLP
WIREFRAME 50
COLOR CPK
SELECT CONT_GLP AND *.CA
LABEL %n%r
SELECT GLP_ATOMS
CPK 100
SELECT GLP_ATOMS AND WATER
LABEL %n
ECHO
ECHO All glucosamine 6-phosphate contacts are displayed
ECHO Press any key to display aminoacids to be replaced

PAUSE
RESTRICT GLP
SPACEFILL OFF
LABELS OFF
SELECT GLP.P
LABEL Glucosamine-6-phosphate
SELECT AA1, AA1_V2, AA2, AA2_V2
WIREFRAME 50
SELECT SELECTED AND GLP_ATOMS
CPK 100
LABEL %n%r%a
SELECT AA1, AA1_V2
COLOR ORANGE
SELECT AA2, AA2_V2
COLOR GREENBLUE
SELECT HOH3, HOH11, HOH18
CPK 100
LABEL %n%r
BOND 1892 2899 +
BOND 1892 2891 +
BOND 2899 2834 +
BOND 2891 2835 +
BOND 2778 2834 +
BOND 2775 2906 +
BOND 2906 2833 +
BOND 842 2841 +
BOND 847 2841 +
BOND 832 2840 +
ECHO
ECHO Aminoacids to be replaced to weaken binding of GLP are in orange
ECHO Aminoacids to be replaced to maintain binding of GLP are in greenblue