Talk:Garman lab: Interconversion of lysosomal enzyme specificities: Difference between revisions

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Line 1: Line 1:
Figure 1 overall
  <nowiki>
  <nowiki>
Figure 1 panel B
load files "=3HG5" "=3H54"
load 3HG5
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 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
</nowiki>
 
Figure X bonus
<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} 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 selected and not _C; spacefill 80; color cpk
select (203,206) and *:A.CB; label %m%r; color label black;
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 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
</nowiki>


load 3HG5
 
restrict none
<nowiki>
select protein; cartoon; color palegreen; center selected
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 801-802; wireframe 100; color cpk
select group within(3.0, (BMA, NAG, MAN)) and sidechain
select protein and 2.1; cartoon; color cornflowerblue;
select selected or (BMA, NAG, MAN)
select 1000,2000; wireframe 100; color cpk
wireframe 50
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 panel C
Figure Y bonus
load 3H54
<nowiki>
load Image:Interconversion_model.pdb # do this in the scene authoring tool
restrict none  # display is cleared
restrict none  # display is cleared
set ssbonds SIDECHAIN
set ssBondsBackbone FALSE
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
# show active site of alpha-GAL
define ~actgal (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A/1
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
select (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA/1
trace 10; color palegreen
select a2g:A; wireframe 60;
select gla:A; wireframe 60;
set fontScaling ON
select (203,206) and *:A.CB/1; label %m%r; color label black;
# show active site of alpha-NAGAL
define ~actnagal (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A/2
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select selected and not _C; spacefill 80; color cpk
select (188,191) and *:A.CB; label %m%r; color label black; font label 20
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA/2;  
select a2g:A; wireframe 60; center selected
trace 10; color cornflowerblue
select (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 a2g:A; wireframe 60;
select (188,191) and *:A.CB/2; label %m%r; color label black; font label 14
# one of the lines below for the four different figures
contact {a2g:A/1}{~actgal} full
 
contact {gla:A/1}{~actgal} full
 
contact {gla:A/2{~actnagal} full


load 3H54
contact {a2g:A/2}{~actnagal} full
restrict none
# hide one of the sugars (depending which contacts we are showing
set hermiteLevel 6; set traceAlpha false
hide a2g
select protein; cartoon; color cornflowerblue; center selected
 
select a2g; wireframe 100; color cpk
hide gla
select group within(3.0, (BMA, NAG, MAN)) and sidechain
</nowiki>
select selected or (BMA, NAG, MAN)
wireframe 50


Figure 2 panel A
Figure 2 panel A
<nowiki>
load 3lx9
load 3lx9
restrict none  # display is cleared
restrict none  # display is cleared
Line 46: Line 132:
select a2g:A; wireframe 60; center selected
select a2g:A; wireframe 60; center selected
isosurface s_one color cornflowerblue "http://proteopedia.org/wiki/images/8/84/3lx9.jvxl" mesh
isosurface s_one color cornflowerblue "http://proteopedia.org/wiki/images/8/84/3lx9.jvxl" mesh
</nowiki>
Figure 2 panel B
<nowiki>
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
</nowiki>
</nowiki>


Figure 2 panel D
Figure 2 panel D
load 3lx9_3h54.pdb‎
<nowiki>
load files "=3H54" "=3LX9"
restrict none  # display is cleared
restrict none  # display is cleared
define ~act2 2.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
define ~act1 1.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE
set ssbonds SIDECHAIN
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 1.1 and ~act1 and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
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 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA;  
select a2g:A/2; wireframe 60; center selected
trace 10; color cornflowerblue
select selected and _C; color skyblue
select 1.1 and 1000:A; wireframe 60;
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA/2; trace 10; color cornflowerblue
select selected and _C; color skyblue;
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 2.1 and ~act2 and (sidechain or *.CA); wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select selected and not _C; spacefill 80; color cpk
select a2g:A/1; wireframe 60; center selected
select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA;
select selected and _C; color gold
trace 10; color yellow
select 2.1 and 1000:A; wireframe 60;  
select selected and _C; color beige; center selected
</nowiki>

Latest revision as of 19:56, 23 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 Y bonus 

load Image:Interconversion_model.pdb # do this in the scene authoring tool
restrict none  # display is cleared
set ssBondsBackbone FALSE
# show active site of alpha-GAL
define ~actgal (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A/1
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
select (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA/1
trace 10; color palegreen
select a2g:A; wireframe 60;
select gla:A; wireframe 60;
set fontScaling ON
select (203,206) and *:A.CB/1; label %m%r; color label black;
# show active site of alpha-NAGAL
define ~actnagal (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A/2
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA/2; 
trace 10; color cornflowerblue
select 801:A; wireframe 60; center selected
select a2g:A; wireframe 60;
select (188,191) and *:A.CB/2; label %m%r; color label black; font label 14
# one of the lines below for the four different figures 
contact {a2g:A/1}{~actgal} full

contact {gla:A/1}{~actgal} full

contact {gla:A/2{~actnagal} full

contact {a2g:A/2}{~actnagal} full
# hide one of the sugars (depending which contacts we are showing
hide a2g

hide gla

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 files "=3H54" "=3LX9"
restrict none  # display is cleared
define ~act2 2.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
define ~act1 1.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE
set ssbonds SIDECHAIN
select 1.1 and ~act1 and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; 
trace 10; color cornflowerblue
select 1.1 and 1000:A; wireframe 60; 
select selected and _C; color skyblue;
select 2.1 and ~act2 and (sidechain or *.CA); wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA; 
trace 10; color yellow
select 2.1 and 1000:A; wireframe 60; 
select selected and _C; color beige; center selected

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis
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