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

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)	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

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