DynDom - Protein Domain Motions

Xylulose Kinase

(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	Xylulose Kinase
Conformer 1 (PDB)	2itm (B)
Conformer 2 (PDB)	2itm (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	392	0.86	3 - 252 256 - 291 296 - 300 368 - 392 398 - 466 469 - 475
2	79	1.35	253 - 255 292 - 295 301 - 367 393 - 397 467 - 468 476 - 482

Sequence

`________________________________________________________________________________________________________________________` `2itm(B) : MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG` `:` `2itm(A) : MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2itm(B) : NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG` `:` `2itm(A) : NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG` `________________________________________________________________________________________________________________________` `________251_255________________________________290_294______________________________________________________________367_` `2itm(B) : VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLS-qAKGVFFGLTHQHGPNELARAVLEG` `:` `2itm(A) : VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSpQAKGVFFGLTHQHGPNELARAVLEG` `________251_255________________________________290_294______________________________________________________________367_` `_____________________392__397__________________________________________________________________466___472____________` `2itm(B) : VGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLLPLMA` `:` `2itm(A) : VGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLLPLMA` `_____________________392__397__________________________________________________________________466___472____________`

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)	12.8
Translation (A)	0.2
Closure (%)	77.2
Bending Residues ( green )	251 - 253 255 - 257 290 - 292 294 - 301 367 - 370 392 - 393 397 - 398 466 - 469 472 - 476
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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