DynDom - Protein Domain Motions

Glycerol 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	Glycerol Kinase
Conformer 1 (PDB)	2d4w (A)
Conformer 2 (PDB)	1bu6 (Y)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	334	3.17	4 - 263 272 - 305 348 - 362 437 - 467 499 - 500
2	155	1.54	264 - 271 306 - 347 363 - 436 468 - 498

Sequence

`________________________________________________________________________________________________________________________` `2d4w(A) : ADYVLAIDQGTTSSRAIVFDHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVGLALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGA` `:` `1bu6(Y) : EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLTKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRD-GL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2d4w(A) : EKY-KSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGTEGGVHVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSSEVYGHGRPRGLVPG--` `:` `1bu6(Y) : EDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMT---QGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGG--KGGT` `________________________________________________________________________________________________________________________` `________________________263_____271________________________________305_______________________________________347________` `2d4w(A) :` `-VPIAGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTV-CYKIGDAPAVYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFA` `:` `1bu6(Y) :` `RIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVN--YALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGA` `________________________262_____270________________________________303_______________________________________345________` `______________________________________________________________________________436____________________________467________` `2d4w(A) : PYWRPDARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVANELLMQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPS` `:` `1bu6(Y) : PYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPG` `______________________________________________________________________________434____________________________465________` `____________________498______` `2d4w(A) : MESGERERLYRNWKKAVTKTMEWVDEDVE` `:` `1bu6(Y) : IETTERNYRYAGWKKAVKRAMAWEEHD*` `____________________496______`

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)	24.9
Translation (A)	-0.7
Closure (%)	96.2
Bending Residues ( green )	263 - 264 271 - 272 305 - 306 347 - 348 350 - 364 436 - 437 467 - 468 498 - 500
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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