Talk:Green Fluorescent Protein

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Contents 1 List of figures: Green_Fluorescent_Protein 1.1 Initial view 1.2 default scene 1.3 secondary structure 1.4 \"stripes\" 1.5 α-helix 1.6 perpendicular 1.7 contacts 1.8 chromophore 1.9 top view 1.10 4-(p-hydroxybenzylidene)-imidazolidin-5-one 1.11 larger conjugated system 1.12 four water molecules 1.13 side chains 1.14 polar interactions 1.15 edge-face interaction 1.16 base 1.17 truncated the ends 1.18 see without truncated ends 1.19 amino terminus 1.20 dimer 1.21 multimers 1.22 Jmol commands: buttons etc 1.22.1 make bonds 1.22.2 Fancy, high-quality cartoons on/off 1.22.3 ⚞Thr 65⚟ 1.22.4 ⚞Tyr 66⚟ 1.22.5 ⚞Gly 67⚟ 1.22.6 Fancy, high-quality cartoons on/off 1.22.7 Fancy, high-quality cartoons on/off 1.23 Summary 1.23.1 coordinates used 2 3D scenes

List of figures: Green_Fluorescent_Protein

Initial view

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_default/2.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?c633a54d03b8b50318876fc5555cdc4c

default scene

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_default/2.spt

coords: same as Initial view

secondary structure

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_barrel/2.spt

coords: same as Initial view

\"stripes\"

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Water_stripes/1.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?a144edeb1a0e1f7ef8ec555f19d99243

α-helix

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Central_helix/1.spt

coords: same as \"stripes\"

perpendicular

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Perpendicular/1.spt

coords: same as \"stripes\"

contacts

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Spacefill/1.spt

coords: same as \"stripes\"

chromophore

script: https://proteopedia.org/wiki/scripts/10/100139/Chromophore/2.spt Available on this page: Green_Fluorescent_Protein

coords: same as \"stripes\"

top view

script: https://proteopedia.org/wiki/scripts/10/100139/Green_fluorescent_protein/1.spt Available on this page: Green_Fluorescent_Protein

coords: same as Initial view

4-(p-hydroxybenzylidene)-imidazolidin-5-one

script: https://proteopedia.org/wiki/scripts/10/100139/Chromophore_structure/3.spt Available on this page: Green_Fluorescent_Protein

coords: same as \"stripes\"

Chromophore structure post-translational modifications

larger conjugated system

script: https://proteopedia.org/wiki/scripts/10/100139/Chromophore/3.spt Available on this page: Green_Fluorescent_Protein

coords: same as \"stripes\"

four water molecules

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Water_molecules/1.spt

coords: same as \"stripes\"

side chains

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Gln69_glu222/1.spt

coords: same as \"stripes\"

polar interactions

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Polar_interactions/2.spt

coords: same as \"stripes\"

edge-face interaction

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Edge_face_interaction/1.spt

coords: same as \"stripes\"

base

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Arg96/1.spt

coords: same as \"stripes\"

truncated the ends

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Truncated_ends/3.spt

coords: same as \"stripes\"

see without truncated ends

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_barrel/2.spt

coords: same as Initial view

amino terminus

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Amino_terminus/2.spt

coords: same as \"stripes\"

dimer

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1gfl/1.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?cef2bb867c0302e8598fb8875c984cf4

multimers

script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1w7s/1.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?22ea3e9e5eef2bdbdb16d8b8ebd93110

Jmol commands: buttons etc

make bonds

select (64.C or 66.N1 or 66.C3 or 68.N); connect 1.1 1.6; select 64, 66, 68; wireframe 0.2;

Fancy, high-quality cartoons on/off

if (~fancyoff); set ribbonborder off; set antialiasdisplay off;~fancyoff=false; else; set ribbonborder on; set antialiasdisplay on; select protein; cartoon on; ~fancyoff=true; endif;\n

⚞Thr 65⚟

select (*.C1, *.CA1, *.N1, *.CB1, *.CG1, *.OG1) and 66; selectionHalos ON; delay 1.5;selectionHalos OFF;

⚞Tyr 66⚟

select (*.C2, *.O2, *.CA2, *.N2, *.CB2, *.CG2, *.CD1, *.CD2, *.CE1, *.CE2, *.CZ, *.OH) and 66; selectionHalos ON; delay 1.5;selectionHalos OFF;

⚞Gly 67⚟

select (*.O3,*.C3,*.CA3,*.N3) and 66; selectionHalos ON; delay 1.5;selectionHalos OFF;

Fancy, high-quality cartoons on/off

if (~fancyoff); set ribbonborder off; set antialiasdisplay off;~fancyoff=false; else; set ribbonborder on; set antialiasdisplay on; select protein; cartoon on; ~fancyoff=true; endif;\n

Fancy, high-quality cartoons on/off

if (~fancyoff); set ribbonborder off; set antialiasdisplay off;~fancyoff=false; else; set ribbonborder on; set antialiasdisplay on; select protein; cartoon on; ~fancyoff=true; endif;\n

Summary

Total of green links: 21

Total of Jmol buttons etc: 7

coordinates used

• 1EMA: https://proteopedia.org/cgi-bin/getfrozenstructure?c633a54d03b8b50318876fc5555cdc4c
• 1EMA: https://proteopedia.org/cgi-bin/getfrozenstructure?a144edeb1a0e1f7ef8ec555f19d99243
• 1GFL: https://proteopedia.org/cgi-bin/getfrozenstructure?cef2bb867c0302e8598fb8875c984cf4
• 1W7S: https://proteopedia.org/cgi-bin/getfrozenstructure?22ea3e9e5eef2bdbdb16d8b8ebd93110

3D scenes

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