Talk:Garman lab: Interconversion of lysosomal enzyme specificities

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Line 1: Line 1:
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Figure 1 panel B
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Figure 1 overall
<nowiki>
<nowiki>
-
load 3HG5
+
load files "=3HG5" "=3H54"
restrict none # display is cleared
restrict none # display is cleared
-
set ssbonds SIDECHAIN
+
# define active site residues and superimpose structures
-
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A; wireframe 60; color bonds palegreen
+
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
 +
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
 +
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE
 +
select protein and 1.1; cartoon; color palegreen; center selected
 +
select 801-802; wireframe 100; color cpk
 +
select protein and 2.1; cartoon; color cornflowerblue;
 +
select 1000,2000; wireframe 100; color cpk
 +
select group within(3.0, (BMA, NAG, MAN)) and (sidechain or *.CA)
 +
select selected or (BMA, NAG, MAN); wireframe 50
 +
model 1 # or model 2
 +
</nowiki>
 +
 
 +
 
 +
Figure 1 active site
 +
<nowiki>
 +
load files "=3HG5" "=3H54"
 +
restrict none # display is cleared
 +
# define active site residues and superimpose structures
 +
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
 +
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
 +
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE
 +
# show active site of alpha-GAL
 +
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
select selected and not _C; spacefill 80; color cpk
 +
select 1.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA
 +
trace 10; color palegreen
 +
select a2g:A; wireframe 60;
set fontScaling ON
set fontScaling ON
-
select (203,206) and *:A.CB; label %m%r; color label black;
+
select 1.1 and (203,206) and *:A.CB; label %m%r; color label black;
 +
# show active site of alpha-NAGAL
 +
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
 +
select selected and not _C; spacefill 80; color cpk
 +
select 2.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA;
 +
trace 10; color cornflowerblue
select 801:A; wireframe 60; center selected
select 801:A; wireframe 60; center selected
-
select (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA; trace 10; color palegreen
+
select 2.1 and (188,191) and *:A.CB; label %m%r; color label black; font label 14
-
 
+
model 1 # or model 2
-
load 3HG5
+
-
restrict none
+
-
select protein; cartoon; color palegreen; center selected
+
-
select 801-802; wireframe 100; color cpk
+
-
select group within(3.0, (BMA, NAG, MAN)) and sidechain
+
-
select selected or (BMA, NAG, MAN)
+
-
wireframe 50
+
</nowiki>
</nowiki>
-
 
+
Figure X bonus
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Figure 1 panel C
+
<nowiki>
<nowiki>
-
load 3H54
+
load files "=3HG5" "=3H54"
restrict none # display is cleared
restrict none # display is cleared
-
set ssbonds SIDECHAIN
+
# define active site residues and superimpose structures
-
select (188,191,158,127,119,78,79,33,217,213,192,154,156) and (sidechain or *.CA) and *:A; wireframe 60; color bonds cornflowerblue
+
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
 +
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
 +
compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE
 +
# show active site of alpha-GAL
 +
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
select selected and not _C; spacefill 80; color cpk
 +
select 1.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA
 +
trace 10; color palegreen
 +
select a2g:A; wireframe 60;
set fontScaling ON
set fontScaling ON
-
select (188,191) and *:A.CB; label %m%r; color label black; font label 20
+
# show active site of alpha-NAGAL
-
select a2g:A; wireframe 60; center selected
+
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
-
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; trace 10; color cornflowerblue
+
select selected and not _C; spacefill 80; color cpk
 +
select 2.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA;
 +
trace 10; color cornflowerblue
 +
select 801:A; wireframe 60; center selected
 +
select 1.1 and (203,206) and *:A.CB; label %m%r; color label black;
 +
select 2.1 and (188,191) and *:A.CB; label %m%r; color label black; font label 14
 +
model 1 # or model 2
 +
 
 +
load files "=3HG5" "=3H54"
 +
restrict none # display is cleared
 +
compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE
 +
select protein and 1.1; cartoon; color palegreen; center selected
 +
select 801-802; wireframe 100; color cpk
 +
select protein and 2.1; cartoon; color cornflowerblue;
 +
select 1000,2000; wireframe 100; color cpk
 +
select group within(3.0, (BMA, NAG, MAN)) and (sidechain or *.CA)
 +
select selected or (BMA, NAG, MAN); wireframe 50
 +
model 1 # or model 2
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load 3H54
 
-
restrict none
 
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set hermiteLevel 6; set traceAlpha false
 
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select protein; cartoon; color cornflowerblue; center selected
 
-
select a2g; wireframe 100; color cpk
 
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select group within(3.0, (BMA, NAG, MAN)) and sidechain
 
-
select selected or (BMA, NAG, MAN)
 
-
wireframe 50
 
</nowiki>
</nowiki>
 +
Figure 2 panel A
Figure 2 panel A

Revision as of 01:26, 4 July 2018

Figure 1 overall 

load files "=3HG5" "=3H54"
restrict none  # display is cleared
# define active site residues and superimpose structures
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE
select protein and 1.1; cartoon; color palegreen; center selected
select 801-802; wireframe 100; color cpk
select protein and 2.1; cartoon; color cornflowerblue;
select 1000,2000; wireframe 100; color cpk
select group within(3.0, (BMA, NAG, MAN)) and (sidechain or *.CA)
select selected or (BMA, NAG, MAN); wireframe 50
model 1 # or model 2


Figure 1 active site 

load files "=3HG5" "=3H54"
restrict none  # display is cleared
# define active site residues and superimpose structures
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE
# show active site of alpha-GAL
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
select 1.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA
trace 10; color palegreen
select a2g:A; wireframe 60;
set fontScaling ON
select 1.1 and (203,206) and *:A.CB; label %m%r; color label black;
# show active site of alpha-NAGAL
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select 2.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; 
trace 10; color cornflowerblue
select 801:A; wireframe 60; center selected
select 2.1 and (188,191) and *:A.CB; label %m%r; color label black; font label 14
model 1 # or model 2

Figure X bonus 

load files "=3HG5" "=3H54"
restrict none  # display is cleared
# define active site residues and superimpose structures
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE
# show active site of alpha-GAL
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
select 1.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA
trace 10; color palegreen
select a2g:A; wireframe 60;
set fontScaling ON
# show active site of alpha-NAGAL
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select 2.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; 
trace 10; color cornflowerblue
select 801:A; wireframe 60; center selected
select 1.1 and (203,206) and *:A.CB; label %m%r; color label black;
select 2.1 and (188,191) and *:A.CB; label %m%r; color label black; font label 14
model 1 # or model 2

load files "=3HG5" "=3H54"
restrict none  # display is cleared
compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE
select protein and 1.1; cartoon; color palegreen; center selected
select 801-802; wireframe 100; color cpk
select protein and 2.1; cartoon; color cornflowerblue;
select 1000,2000; wireframe 100; color cpk
select group within(3.0, (BMA, NAG, MAN)) and (sidechain or *.CA)
select selected or (BMA, NAG, MAN); wireframe 50
model 1 # or model 2


Figure 2 panel A 

load 3lx9
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A; wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CB; label %m%r; color label black;
select a2g:A; wireframe 60; center selected
isosurface s_one color cornflowerblue "http://proteopedia.org/wiki/images/8/84/3lx9.jvxl" mesh

Figure 2 panel B 

load 3lxa
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A; wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CB; label %m%r; color label black
select 801:A; wireframe 60; center selected

Figure 2 panel D 

load 3lx9_3h54.pdb‎
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (188,191,158,127,119,78,79,33,217,213,192,154,156) and (sidechain or *.CA) and *:A/2; wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select (188,191) and *:A.CB/2; label %m%r; color label black; font label 20
select a2g:A/2; wireframe 60; center selected
select selected and _C; color skyblue
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA/2; trace 10; color cornflowerblue
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A/1; wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select a2g:A/1; wireframe 60; center selected
select selected and _C; color gold

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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