Talk:Kisker lab: 5B5Q

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Scripts used

Panel C:

load 1EUV
select :A
color skyblue
select :B
color orange
select 511-513
color yellow
cartoon 0.3

Panel D:

load 1XT9
cartoon only
select :A
color white
select :B
color mediumorchid
select 92-102
color yellow
cartoon 0.3
set zshade on
set zshadepower 2

Panel E:

sselect all; cartoon only; color silver
select :B/2; hide selected

# color CDUB1 like panel A and show catalytic triad
select :a/2; color lime
select 249-273; color yellow
select (275,345,292) and (sidechain or *.CA) and not _H; wireframe 100%
select selected and not _C; color CPK

# color the related deubiquitinase like panel C
select :B/1; color orchid
select 70-76:B/1; wireframe only; wireframe 100%
select selected and not _C; color CPK
select (102:A/1, 163:A/1, 119:A/1) and (sidechain or *.CA) and not _H; wireframe 100%
select selected and not _C; color CPK

# add the covelent enzyme-substrate bond
select 76:B.C,163.SG; connect 1.9 (selected)(selected); wireframe 100%

Bonus:

select all
cartoon only
color silver
select 275,292,345 and sidechain
wireframe 0.3
select 345 and sidechain
color yellow
center selected
select protein and within(10.0, 271) and not 249-273
isosurface ignore(solvent or 249-273) molecular MAP property color
select 254-270
trace only
color skyblue
select 271 and (sidechain or *.CA) and _C
wireframe 0.5