DynDom - Protein Domain Motions

Topoisomerase V

(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 V
Conformer 1 (PDB)	2csd (A)
Conformer 2 (PDB)	2csb (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	143	1.39	294 - 417 419 - 431 448 - 455
2	283	0.97	5 - 291
3	78	0.66	418 - 418 432 - 447 456 - 516

Sequence

`________________________________________________________________________________________________________________________` `2csd(A) : LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDE` `:` `2csb(B) : LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYL-eRSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2csd(A) : EDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERT` `:` `2csb(B) : EDVPAIEVRAVKRNPLQPALYRILVRYGRVDL-pVTVDEVPPE-aGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERT` `________________________________________________________________________________________________________________________` `______________________________________________291_______________________________________________________________________` `2csd(A) : AKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGL` `:` `2csb(B) : AKRHVKRRDRLLEELYEHLEELSERYLRHPLTRRWIVEHKRDI-rRYLEQRIVECALKLQDRYGIREDVALCLARAFDGSIS-iATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHGL` `______________________________________________291_______________________________________________________________________` `____________________________________________________417___________431_____________447____454____________________________` `2csd(A) : SPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAE` `:` `2csb(B) : SPDAADELIEHFESIAGILATDLEEIER-yEEGRLSEEAYRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGYASLISIRGIDRERAE` `____________________________________________________417___________431_____________447____454____________________________` `_____________________________________` `2csd(A) : RLLKKYGGYSKVREAGVEELREDGLTDAQIRELKGL*` `:` `2csb(B) : RLLKKYGGYSKVREAGVEELREDGLTDAQIRELKGLK` `_____________________________________`

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)	16.4
Translation (A)	0.5
Closure (%)	17.3
Bending Residues ( green )	291 - 294
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	8.6
Translation (A)	-0.4
Closure (%)	58.3
Bending Residues ( green )	417 - 419 431 - 432 447 - 448 454 - 456
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Shear

PyMOL Script

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