Talk:Kisker lab: 5B5Q

From Proteopedia

Scripts used

Panel A:

select all; cartoon only; color yellowgreen
select 249-273; color yellow
select (275,292,345) and (*.CA or sidechain) and not hydrogen; wireframe .3;
select selected and not *.CA; color cpk

Panel B:

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

Panel C:

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 D:

select all; cartoon only; color yellow
select (275,292,345) and not hydrogen; wireframe .3;
select selected and not _C; color cpk
select (275,292,345) and *.SG; color goldenrod
set zshade on
set zshadepower 2

Electron density:

Get electron density from PDBe: https://www.ebi.ac.uk/pdbe/entry/pdb/5b5q

Use jmol app to create surface file:
isosurface s_one color blue within 1.5 {(275:A,292:A,345:A)} "5b5q.ccp4." mesh nofill; write map.jvxl

Load surface using script:

isosurface s_one color silver "http://proteopedia.org/wiki/images/6/61/Map.jvxl" mesh

Panel E:

This figure uses a superposition of 1xt9 and 5b5q made outside of proteopedia and uploaded as Image:3lx9 3h54.pdb

load /cgi-bin/getfrozenstructure?1xt9_5b5q.pdb 
#This file contains the two proteins as model 1 and model 2
#The superposition was done in UCSF Chimera, and the file uploaded to proteopedia
 
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 covalent enzyme-substrate bond
select 76:B.C,163.SG; connect 1.9 (selected)(selected); wireframe 100%

# show the hydrogen bonding
select 101/1 and backbone; wireframe 100; center selected; color cpk
select 101,76; calculate hbonds; hbonds 0.1
select 274:A/2 and backbone and not hydrogen; wireframe 100; color yellow
select selected and not _C; color cpk
set echo ID hb {101:A.O/1 or 76:B.N/1}
echo "3.1 Å"

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(not selected) molecular MAP property color
select 254-270; trace only; color yellow
select 271 and (sidechain or *.CA) and _C; wireframe 0.5
select 271.CB; label "%r%n"; color label black