DynDom - Protein Domain Motions

Protein (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	Protein (Dna Topoisomerase I)
Conformer 1 (PDB)	1a35 (A)
Conformer 2 (PDB)	1ej9 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	417	0.66	217 - 252 256 - 256 261 - 262 281 - 282 291 - 291 294 - 300 308 - 368 372 - 419 422 - 760
2	47	0.47	253 - 255 257 - 260 263 - 280 283 - 290 292 - 293 301 - 307 369 - 371 420 - 421

Sequence

`_______________________________________________252_____260_________________280_______290_______300____307_______________` `1a35(A) : ************IKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKE` `:` `1ej9(A) : WKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKE` `_______________________________________________252_____260_________________280_______290_______300____307_______________` `___________________________________________368________________________________________________419_______________________` `1a35(A) : EKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQ` `:` `1ej9(A) : EKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQ` `___________________________________________368________________________________________________419_______________________` `________________________________________________________________________________________________________________________` `1a35(A) : KYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPED` `:` `1ej9(A) : KYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPED` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1a35(A) : DLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAqIALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMA` `:` `1ej9(A) : DLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNH---QiALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMA` `________________________________________________________________________________________________________________________` `______` `1a35(A) : DEDYEF` `:` `1ej9(A) : DEDYEF` `______`

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)	5.7
Translation (A)	0.1
Closure (%)	77.2
Bending Residues ( green )	252 - 253 255 - 257 260 - 263 280 - 283 290 - 294 300 - 301 307 - 308 368 - 369 371 - 372 419 - 424
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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