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Talk:Green Fluorescent Protein

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(New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...)
Current revision (14:04, 22 September 2020) (edit) (undo)
 
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==Your Heading Here (maybe something like 'Structure')==
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==List of figures: Green_Fluorescent_Protein==
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<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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This is a default text for your page '''Green Fluorescent Protein'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
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== Function ==
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===Initial view===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_default/2.spt
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== Disease ==
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coords: https://proteopedia.org/cgi-bin/getfrozenstructure?c633a54d03b8b50318876fc5555cdc4c
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== Relevance ==
 
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== Structural highlights ==
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===default scene===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_default/2.spt
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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coords: same as Initial view
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===secondary structure===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_barrel/2.spt
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coords: same as Initial view
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===\"stripes\"===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Water_stripes/1.spt
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coords: https://proteopedia.org/cgi-bin/getfrozenstructure?a144edeb1a0e1f7ef8ec555f19d99243
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===α-helix===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Central_helix/1.spt
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coords: same as \"stripes\"
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===perpendicular===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Perpendicular/1.spt
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coords: same as \"stripes\"
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===contacts===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Spacefill/1.spt
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coords: same as \"stripes\"
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===chromophore===
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script: https://proteopedia.org/wiki/scripts/10/100139/Chromophore/2.spt
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Available on this page: Green_Fluorescent_Protein
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coords: same as \"stripes\"
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 +
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===top view===
 +
script: https://proteopedia.org/wiki/scripts/10/100139/Green_fluorescent_protein/1.spt
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Available on this page: Green_Fluorescent_Protein
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coords: same as Initial view
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 +
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===4-(p-hydroxybenzylidene)-imidazolidin-5-one===
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script: https://proteopedia.org/wiki/scripts/10/100139/Chromophore_structure/3.spt
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Available on this page: Green_Fluorescent_Protein
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coords: same as \"stripes\"
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<blockquote>Chromophore structure post-translational modifications</blockquote>
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===larger conjugated system===
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script: https://proteopedia.org/wiki/scripts/10/100139/Chromophore/3.spt
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Available on this page: Green_Fluorescent_Protein
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coords: same as \"stripes\"
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===four water molecules===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Water_molecules/1.spt
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coords: same as \"stripes\"
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===side chains===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Gln69_glu222/1.spt
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coords: same as \"stripes\"
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===polar interactions===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Polar_interactions/2.spt
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coords: same as \"stripes\"
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===edge-face interaction===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Edge_face_interaction/1.spt
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coords: same as \"stripes\"
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===base===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Arg96/1.spt
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coords: same as \"stripes\"
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===truncated the ends===
 +
script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Truncated_ends/3.spt
 +
 +
coords: same as \"stripes\"
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 +
===see without truncated ends===
 +
script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_barrel/2.spt
 +
 +
coords: same as Initial view
 +
 +
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===amino terminus===
 +
script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/Amino_terminus/2.spt
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coords: same as \"stripes\"
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===dimer===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1gfl/1.spt
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coords: https://proteopedia.org/cgi-bin/getfrozenstructure?cef2bb867c0302e8598fb8875c984cf4
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===multimers===
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script: https://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1w7s/1.spt
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coords: https://proteopedia.org/cgi-bin/getfrozenstructure?22ea3e9e5eef2bdbdb16d8b8ebd93110
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===Jmol commands: buttons etc===
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====make bonds====
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select (64.C or 66.N1 or 66.C3 or 68.N); connect 1.1 1.6; select 64, 66, 68; wireframe 0.2;
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====Fancy, high-quality cartoons on/off====
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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
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====⚞Thr 65⚟====
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select (*.C1, *.CA1, *.N1, *.CB1, *.CG1, *.OG1) and 66; selectionHalos ON; delay 1.5;selectionHalos OFF;
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====⚞Tyr 66⚟====
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select (*.C2, *.O2, *.CA2, *.N2, *.CB2, *.CG2, *.CD1, *.CD2, *.CE1, *.CE2, *.CZ, *.OH) and 66; selectionHalos ON; delay 1.5;selectionHalos OFF;
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====⚞Gly 67⚟====
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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
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===Summary===
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Total of green links: 21
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Total of Jmol buttons etc: 7
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====coordinates used====
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*1EMA: https://proteopedia.org/cgi-bin/getfrozenstructure?c633a54d03b8b50318876fc5555cdc4c
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*1EMA: https://proteopedia.org/cgi-bin/getfrozenstructure?a144edeb1a0e1f7ef8ec555f19d99243
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*1GFL: https://proteopedia.org/cgi-bin/getfrozenstructure?cef2bb867c0302e8598fb8875c984cf4
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*1W7S: https://proteopedia.org/cgi-bin/getfrozenstructure?22ea3e9e5eef2bdbdb16d8b8ebd93110
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==3D scenes==
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<StructureSection load='' size='350' side='right' caption='' scene=''><scene name='Green_Fluorescent_Protein/1ema_gfp_default/2'>Green_Fluorescent_Protein/1ema_gfp_default/2</scene>
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<scene name='Green_Fluorescent_Protein/1ema_gfp_default/2'>Green_Fluorescent_Protein/1ema_gfp_default/2</scene>
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<scene name='Green_Fluorescent_Protein/1ema_gfp_barrel/2'>Green_Fluorescent_Protein/1ema_gfp_barrel/2</scene>
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<scene name='Green_Fluorescent_Protein/Water_stripes/1'>Green_Fluorescent_Protein/Water_stripes/1</scene>
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<scene name='Green_Fluorescent_Protein/Central_helix/1'>Green_Fluorescent_Protein/Central_helix/1</scene>
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<scene name='Green_Fluorescent_Protein/Perpendicular/1'>Green_Fluorescent_Protein/Perpendicular/1</scene>
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<scene name='Green_Fluorescent_Protein/Spacefill/1'>Green_Fluorescent_Protein/Spacefill/1</scene>
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<scene name='10/100139/Chromophore/2'>10/100139/Chromophore/2</scene>
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<scene name='10/100139/Green_fluorescent_protein/1'>10/100139/Green_fluorescent_protein/1</scene>
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<scene name='10/100139/Chromophore_structure/3'>10/100139/Chromophore_structure/3</scene>
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<scene name='10/100139/Chromophore/3'>10/100139/Chromophore/3</scene>
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<scene name='Green_Fluorescent_Protein/Water_molecules/1'>Green_Fluorescent_Protein/Water_molecules/1</scene>
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<scene name='Green_Fluorescent_Protein/Gln69_glu222/1'>Green_Fluorescent_Protein/Gln69_glu222/1</scene>
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<scene name='Green_Fluorescent_Protein/Polar_interactions/2'>Green_Fluorescent_Protein/Polar_interactions/2</scene>
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<scene name='Green_Fluorescent_Protein/Edge_face_interaction/1'>Green_Fluorescent_Protein/Edge_face_interaction/1</scene>
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<scene name='Green_Fluorescent_Protein/Arg96/1'>Green_Fluorescent_Protein/Arg96/1</scene>
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<scene name='Green_Fluorescent_Protein/Truncated_ends/3'>Green_Fluorescent_Protein/Truncated_ends/3</scene>
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<scene name='Green_Fluorescent_Protein/1ema_gfp_barrel/2'>Green_Fluorescent_Protein/1ema_gfp_barrel/2</scene>
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<scene name='Green_Fluorescent_Protein/Amino_terminus/2'>Green_Fluorescent_Protein/Amino_terminus/2</scene>
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<scene name='Green_Fluorescent_Protein/1gfl/1'>Green_Fluorescent_Protein/1gfl/1</scene>
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<scene name='Green_Fluorescent_Protein/1w7s/1'>Green_Fluorescent_Protein/1w7s/1</scene>
</StructureSection>
</StructureSection>
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== References ==
 
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<references/>
 

Current revision

Contents

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

3D scenes

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Dana Emmert

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