DynDom - Protein Domain Motions

DNA Topoisomerase I

(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	DNA Topoisomerase I
Conformer 1 (PDB)	1r49 (A)
Conformer 2 (PDB)	1k4t (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	481	1.07	206 - 645 706 - 763
2	60	0.71	646 - 705

Sequence

`________________________________________________________________________________________________________________________` `1r49(A) : *KWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMS` `:` `1k4t(A) : QKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1r49(A) : KEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCS-dAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD` `:` `1k4t(A) : KEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1r49(A) : WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGRDSIRYYNKVPVEKRVFKNLQLFMENKQP` `:` `1k4t(A) : WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQP` `________________________________________________________________________________________________________________________` `_____________________________________________________________624________________________________________________________` `1r49(A) : EDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ----------mMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKT` `:` `1k4t(A) : EDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKT` `_____________________________________________________________624________________________________________________________` `______________________705____________________________________________________________` `1r49(A) : KKVVESKKKAVQRLEEQLMKLEVQATDREENKQ-----sKLNFLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF` `:` `1k4t(A) : KKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLN-lDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF` `______________________705____________________________________________________________`

Morph

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jsmol/j2s/core/core.z.js

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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__258344884795503__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet__258344884795503__)

vwrOptions:

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setting document base to "https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do;jsessionid=cda11dd0e7137684226696168506?ddid=DNATO1R3&action=view"

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)

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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

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Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet__258344884795503__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(dyndommorphdb/DNATO1R3.pdb)

FileManager opening 1 https://dyndom.cmp.uea.ac.uk/dyndom/dyndommorphdb/DNATO1R3.pdb

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 206- 645, 706- 763

#jmolScript: color [0 ,0 ,255]

#jmolScript: select 646- 705

#jmolScript: color [255,0 ,0 ]

#jmolScript: select 766- 796

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#jmolScript: backbone 100;

#jmolScript: select 797- 810

#jmolScript: color [255,0 ,0 ]

#jmolScript: backbone 100;

#jmolScript: select 624- 646

#jmolScript: color [0 ,255,0 ]

#jmolScript: select 705- 706

#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

ISOMERASE/DNA 03-OCT-03 1R49

HUMAN TOPOISOMERASE I (TOPO70) DOUBLE MUTANT K532R/Y723F

found biomolecule 1: B, C, A

biomolecule 1: number of transforms: 1

jsmol/j2s/core/coresym.z.js

-- required by ClazzNode ajax=true async=false

Time for openFile(dyndommorphdb/DNATO1R3.pdb): 3077 ms

reading 109368 atoms

ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false

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

Default Van der Waals type for model set to Jmol

109368 atoms created

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

ISOMERASE/DNA 03-OCT-03 1R49

HUMAN TOPOISOMERASE I (TOPO70) DOUBLE MUTANT K532R/Y723F

found biomolecule 1: B, C, A

Adding embedded #jmolscript: select ({4512:4556});backbone only;select ({9069:9113});backbone only;select ({13626:13670});backbone only;select ({18183:18227});backbone only;select ({22740:22784});backbone only;select ({27297:27341});backbone only;select ({31854:31898});backbone only;select ({36411:36455});backbone only;select ({40968:41012});backbone only;select ({45525:45569});backbone only;select ({50082:50126});backbone only;select ({54639:54683});backbone only;select ({59196:59240});backbone only;select ({63753:63797});backbone only;select ({68310:68354});backbone only;select ({72867:72911});backbone only;select ({77424:77468});backbone only;select ({81981:82025});backbone only;select ({86538:86582});backbone only;select ({91095:91139});backbone only;select ({95652:95696});backbone only;select ({100209:100253});backbone only;select ({104766:104810});backbone only;select ({109323:109367});backbone only;select *; select all; color grey; background white; select 206- 645, 706- 763; color [0 ,0 ,255]; select 646- 705; color [255,0 ,0 ]; select 766- 796; color [0 ,0 ,255]; backbone 100; select 797- 810; color [255,0 ,0 ]; backbone 100; select 624- 646; color [0 ,255,0 ]; select 705- 706; 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

24 models

jsmol/j2s/J/thread/AnimationThread.js

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jsmol/j2s/J/g3d/HermiteRenderer.js

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jsmol/j2s/core/coretext.z.js

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DynDom

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	14.9
Translation (A)	-1.8
Closure (%)	56.5
Bending Residues ( green )	624 - 646 705 - 706
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Mixed

PyMOL Script

Download and extract PyMOL PML script file

DNA Topoisomerase I

DynDom run details

Domains

Sequence

Morph

Domain Pairs

Dynamic Contact Graph

Full-size image

Conformer 1 Contact:Residue 1 ———› Residue 2

Conformer 2 Contact:Residue 2 ———› Residue 1

Movement classification: Mixed

PyMOL Script

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1