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