DynDom - Protein Domain Motions

Type II DNA Topoisomerase Vi Subunit B

(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	Type II DNA Topoisomerase Vi Subunit B
Conformer 1 (PDB)	1z5b (B)
Conformer 2 (PDB)	2hkj (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	279	2.15	27 - 92 95 - 95 103 - 103 112 - 315 345 - 348 376 - 378
2	167	1.54	12 - 26 93 - 94 100 - 102 104 - 111 316 - 344 349 - 375 379 - 461

Sequence

`_____________________26________________________________________________________________92_______________________________` `1z5b(B) : KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQ` `:` `2hkj(A) : ****LSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQ` `_____________________26________________________________________________________________92_______________________________` `________________________________________________________________________________________________________________________` `1z5b(B) : DKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKI` `:` `2hkj(A) : DKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKI` `________________________________________________________________________________________________________________________` `_____________________________________________________________307__________________________________344_348_______________` `1z5b(B) : LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIP` `:` `2hkj(A) : LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIP` `_____________________________________________________________307__________________________________344_348_______________` `_________375_______________________________________________________________________________________________` `1z5b(B) : VGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEKRKEQE*****` `:` `2hkj(A) : VGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLA` `_________375_______________________________________________________________________________________________`

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)	17.5
Translation (A)	-0.2
Closure (%)	98.2
Bending Residues ( green )	26 - 27 92 - 112 307 - 316 344 - 346 348 - 349 375 - 376 378 - 379
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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