DynDom - Protein Domain Motions

Lysyl-Trna Synthetase

(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	Lysyl-Trna Synthetase
Conformer 1 (PDB)	1e22 (A)
Conformer 2 (PDB)	1lyl (B)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	216	0.5	164 - 166 171 - 171 175 - 181 185 - 291 296 - 318 395 - 395 422 - 453 457 - 492 494 - 499
2	143	0.38	17 - 151 167 - 170 174 - 174 183 - 184 493 - 493
3	106	0.39	292 - 295 319 - 394 396 - 418 454 - 456

Sequence

`________________________________________________________________________________________________________________________` `1e22(A) : AIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKT` `:` `1lyl(B) : ***FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKT` `________________________________________________________________________________________________________________________` `__________________151__________170________181___________________________________________________________________________` `1e22(A) : QTGELSIHCTELRLLTKALRPLPd-QEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFE` `:` `1lyl(B) : QTGELSIHCTELRLLTKALRPLPDdQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFE` `__________________151__________170________181___________________________________________________________________________` `________________________________291_295____________________318__________________________________________________________` `1e22(A) : INRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFD` `:` `1lyl(B) : INRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFD` `________________________________291_295____________________318__________________________________________________________` `_______________394_____________________418________________________________453____________________________________492____` `1e22(A) : EVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVIL` `:` `1lyl(B) : EVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVIL` `_______________394_____________________418________________________________453____________________________________492____` `______` `1e22(A) : FPAMRP` `:` `1lyl(B) : FPAMRP` `______`

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__596063046984228__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet__596063046984228__)

vwrOptions:

{ "name":"jmolApplet","applet":true,"documentBase":"https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do?action=view&ddid=LYSYL1R3","platform":"J.awtjs2d.Platform","fullName":"jmolApplet__596063046984228__","codePath":"https://dyndom.cmp.uea.ac.uk/dyndom/jsmol/j2s/","display":"jmolApplet_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"596063046984228","bgcolor":"#FFFFFF" }

setting document base to "https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do?action=view&ddid=LYSYL1R3"

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__596063046984228__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(dyndommorphs/LYSYL1R3_JSMOLSCRPT)

FileManager opening 1 https://dyndom.cmp.uea.ac.uk/dyndom/dyndommorphs/LYSYL1R3_JSMOLSCRPT

The Resolver thinks Pdb

jsmol/j2s/core/corebio.z.js

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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 164- 166, 171- 171, 175- 181, 185- 291, 296- 318, 395- 395, 422- 453, 457- 492, 494- 499

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#jmolScript: select 17- 151, 167- 170, 174- 174, 183- 184, 493- 493

#jmolScript: color [255,0 ,0 ]

#jmolScript: select 503- 524

#jmolScript: color [0 ,0 ,255]

#jmolScript: backbone 100;

#jmolScript: select 525- 538

#jmolScript: color [255,0 ,0 ]

#jmolScript: backbone 100;

#jmolScript: select 292- 295, 319- 394, 396- 418, 454- 456

#jmolScript: color [255,255,0 ]

#jmolScript: select 539- 569

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#jmolScript: backbone 100;

#jmolScript: select 570- 583

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#jmolScript: select 164- 167, 171- 174, 181- 183, 492- 493

#jmolScript: color [0 ,255,0 ]

#jmolScript: select 151- 166, 170- 171, 174- 175, 184- 185, 493- 494

#jmolScript: color [0 ,255,0 ]

#jmolScript: select 291- 292, 318- 319, 395- 396, 453- 454

#jmolScript: color [0 ,255,0 ]

#jmolScript: select 295- 296, 394- 395, 418- 422, 456- 457

#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/LYSYL1R3_JSMOLSCRPT): 735 ms

reading 7739 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

7739 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 ({3801:3881});backbone only;select ({7658:7738});backbone only;select *; select all; color grey; background white; select 164- 166, 171- 171, 175- 181, 185- 291, 296- 318, 395- 395, 422- 453, 457- 492, 494- 499; color [0 ,0 ,255]; select 17- 151, 167- 170, 174- 174, 183- 184, 493- 493; color [255,0 ,0 ]; select 503- 524; color [0 ,0 ,255]; backbone 100; select 525- 538; color [255,0 ,0 ]; backbone 100; select 292- 295, 319- 394, 396- 418, 454- 456; color [255,255,0 ]; select 539- 569; color [0 ,0 ,255]; backbone 100; select 570- 583; color [255,255,0 ]; backbone 100; select 164- 167, 171- 174, 181- 183, 492- 493; color [0 ,255,0 ]; select 151- 166, 170- 171, 174- 175, 184- 185, 493- 494; color [0 ,255,0 ]; select 291- 292, 318- 319, 395- 396, 453- 454; color [0 ,255,0 ]; select 295- 296, 394- 395, 418- 422, 456- 457; 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

1e22 (A)

jsmol/j2s/core/corescriptmath.z.js

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jsmol/j2s/JV/PropertyManager.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/core/coreprop.z.js

-- required by JV.PropertyManager ajax=true async=false

1lyl (B)

Script completed

Jmol script terminated

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	4.1
Translation (A)	-0.3
Closure (%)	96.9
Bending Residues ( green )	151 - 167 170 - 175 181 - 185 492 - 494
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	3.5
Translation (A)	0.0
Closure (%)	94.7
Bending Residues ( green )	291 - 292 295 - 296 318 - 319 394 - 396 418 - 422 453 - 454 456 - 457
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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