DynDom - Protein Domain Motions

Phosphoenolpyruvate Carboxykinase

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

Property	Value
Name	Phosphoenolpyruvate Carboxykinase
Conformer 1 (PDB)	1oen
Conformer 2 (PDB)	1os1 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	360	0.93	8 - 90 93 - 236 253 - 258 261 - 357 407 - 436
2	160	2.14	91 - 92 237 - 252 259 - 260 358 - 406 437 - 538

Sequence

`_____________________________________________________________________________________90_________________________________` `1oen : **GLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDA` `:` `1os1(A) : NNGLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDA` `_____________________________________________________________________________________90_________________________________` `______________________________________________________________________________________________________________236_______` `1oen : FCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEAGDV` `:` `1os1(A) : FCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDV` `______________________________________________________________________________________________________________236_______` `______252______________________________________________________________________________________________________357______` `1oen : AVFFGLSGSGKTTLSTDPARRLIGDDEHGWDDDGVFNFEGGSYAKTIKLSKEAEPEIYAAIRRDALLENVTVRAGGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTAD` `:` `1os1(A) : AVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTAD` `______252______________________________________________________________________________________________________357______` `________________________________________406__________________________435________________________________________________` `1oen : AFGVLPPVSRLTADQTQYHFLSGFTAAAA--------pTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISAADTRAIIDAILNGSLDNAETFTLPMFNLAIP` `:` `1os1(A) : AFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIP` `________________________________________406__________________________435________________________________________________` `_________________________________________________________` `1oen : TELPGVDTGILDPRNTYaG---WQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPAL` `:` `1os1(A) : TELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL` `_________________________________________________________`

Morph

jsmol/j2s/core/package.js

-- required by ClazzNode ajax=false async=true

jsmol/j2s/core/core.z.js

-- required by ClazzNode ajax=false async=true

jsmol/j2s/J/g3d/PixelatorT.js

-- required by J.g3d.Graphics3D ajax=false async=true

JSmol exec jmolApplet start applet null

Jmol JavaScript applet jmolApplet__815627713247225__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet__815627713247225__)

vwrOptions:

{ "name":"jmolApplet","applet":true,"documentBase":"https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do?action=view&ddid=PHOSP22R1","platform":"J.awtjs2d.Platform","fullName":"jmolApplet__815627713247225__","codePath":"https://dyndom.cmp.uea.ac.uk/dyndom/jsmol/j2s/","display":"jmolApplet_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"815627713247225","bgcolor":"#FFFFFF" }

setting document base to "https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do?action=view&ddid=PHOSP22R1"

Jmol Version: 14.2.12_2015.02.11 2015-02-11 06:00

java.vendor: Java2Script (HTML5)

java.version: 2014-12-19 08:17:57 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet (signed)

jsmol/j2s/core/corescript.z.js

-- required by ClazzNode ajax=true async=false

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet__815627713247225__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(dyndommorphs/PHOSP22R1_JSMOLSCRPT)

FileManager opening 1 https://dyndom.cmp.uea.ac.uk/dyndom/dyndommorphs/PHOSP22R1_JSMOLSCRPT

The Resolver thinks Pdb

jsmol/j2s/core/corebio.z.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/J/render/MeshRenderer.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

jsmol/j2s/J/shape/Mesh.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

jsmol/j2s/J/renderbio/RocketRenderer.js

-- required by J.renderbio.RocketsRenderer ajax=true async=false

#jmolScript: select all; color grey; background white;

#jmolScript: select 8- 90, 93- 236, 253- 258, 261- 357, 407- 436

#jmolScript: color [0 ,0 ,255]

#jmolScript: select 91- 92, 237- 252, 259- 260, 358- 406, 437- 538

#jmolScript: color [255,0 ,0 ]

#jmolScript: select 541- 559

#jmolScript: color [0 ,0 ,255]

#jmolScript: backbone 100;

#jmolScript: select 560- 573

#jmolScript: color [255,0 ,0 ]

#jmolScript: backbone 100;

#jmolScript: select 90- 91, 236- 237, 255- 259, 357- 358, 435- 437

#jmolScript: color [0 ,255,0 ]

#jmolScript: select 92- 93, 252- 253, 260- 265, 406- 407

#jmolScript: color [0 ,255,0 ]

#jmolScript: select all

#jmolScript: anim mode loop 0.5 0.5;anim on;

#jmolScript: set echo top left;color echo [x0D0D99];echo "DynDom"

#jmolScript: set antialiasDisplay ON

Time for openFile(dyndommorphs/PHOSP22R1_JSMOLSCRPT): 971 ms

reading 8159 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

2 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

8159 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.12_2015.02.11 2015-02-11 06:00 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

Jmol 14.2.12_2015.02.11 2015-02-11 06:00 DSSP analysis for model 1.2 - null

null

Adding embedded #jmolscript: select ({4034:4066});backbone only;select ({8126:8158});backbone only;select *; select all; color grey; background white; select 8- 90, 93- 236, 253- 258, 261- 357, 407- 436; color [0 ,0 ,255]; select 91- 92, 237- 252, 259- 260, 358- 406, 437- 538; color [255,0 ,0 ]; select 541- 559; color [0 ,0 ,255]; backbone 100; select 560- 573; color [255,0 ,0 ]; backbone 100; select 90- 91, 236- 237, 255- 259, 357- 358, 435- 437; color [0 ,255,0 ]; select 92- 93, 252- 253, 260- 265, 406- 407; color [0 ,255,0 ]; select all; anim mode loop 0.5 0.5;anim on; set echo top left;color echo [x0D0D99];echo "DynDom"; set antialiasDisplay ON

2 models

jsmol/j2s/J/thread/AnimationThread.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/J/g3d/HermiteRenderer.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/core/coretext.z.js

-- required by ClazzNode ajax=true async=false

DynDom

Morph animation in progress.
Status: Progress file not found. You may be seeing this after system maintenance due toan issue with some browsers. Please try closing and reopening your browser, or clearingyour browser's cookies. If this issue persists please contact us.

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	19.7
Translation (A)	0.1
Closure (%)	98.8
Bending Residues ( green )	90 - 93 236 - 237 252 - 253 255 - 265 357 - 358 406 - 407 435 - 437
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: missing

PyMOL Script

Download and extract PyMOL PML script file