DynDom - Protein Domain Motions

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	Topoisomerase I
Conformer 1 (PDB)	1a31 (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	225	0.56	217 - 235 237 - 237 309 - 309 334 - 356 364 - 368 374 - 430 432 - 437 442 - 448 473 - 476 485 - 546 550 - 578 583 - 589 720 - 722 726 - 726
2	88	0.65	236 - 236 238 - 308 310 - 313 357 - 363 369 - 373
3	120	0.53	431 - 431 438 - 441 449 - 472 477 - 484 547 - 549 579 - 582 590 - 626 724 - 725 727 - 763

Sequence

`________________________________235______________________________________________________________________308__313_______` `1a31(A) : **************IKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMS` `:` `1k4t(A) : QKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMS` `________________________________235______________________________________________________________________308__313_______` `_____________________________352______361____368__373______________________________________________________430____437_44` `1a31(A) : KEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD` `:` `1k4t(A) : KEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKD` `_____________________________352______361____368__373______________________________________________________430____437_44` `1____448_____________________472_476_____484___________________________________________________________546______________` `1a31(A) : WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQP` `:` `1k4t(A) : WQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQP` `1____448_____________________472_476_____484___________________________________________________________546______________` `_______________578_582____589_________________________________625_______________________________________________________` `1a31(A) : EDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAV------------------------------------------------------` `:` `1k4t(A) : EDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKT` `_______________578_582____589_________________________________625_______________________________________________________` `____________________________________________________________________________________` `1a31(A) :` `---------------------------------------kLNlDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF` `:` `1k4t(A) :` `KKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNlDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF` `____________________________________________________________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	7.6
Translation (A)	0.0
Closure (%)	50.2
Bending Residues ( green )	235 - 238 308 - 310 313 - 334 352 - 358 361 - 364 368 - 369 373 - 374
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	4.4
Translation (A)	-0.2
Closure (%)	93.1
Bending Residues ( green )	430 - 432 437 - 438 441 - 442 448 - 449 472 - 473 476 - 477 484 - 485 546 - 547 549 - 550 578 - 579 582 - 583 589 - 590 625 - 727
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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