DynDom - Protein Domain Motions

Poly(a) Polymerase

(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	Poly(a) Polymerase
Conformer 1 (PDB)	2hhp (A)
Conformer 2 (PDB)	2o1p (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	347	0.83	6 - 224 232 - 315 319 - 354 386 - 389 521 - 524
2	157	1.17	225 - 231 316 - 318 355 - 385 390 - 520 525 - 528

Sequence

`________________________________________________________________________________________________________________________` `2hhp(A) : QKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSL` `:` `2o1p(A) : QKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSL` `________________________________________________________________________________________________________________________` `__________________________________________________________________________________________________224____231____________` `2hhp(A) : LRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARI` `:` `2o1p(A) : LRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARI` `__________________________________________________________________________________________________224____231____________` `_____________________________________________________________________315____________________________________354_________` `2hhp(A) : CQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLE` `:` `2o1p(A) : CQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLE` `_____________________________________________________________________315____________________________________354_________` `___________________385_389______________________________________________________________________________________________` `2hhp(A) : ITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALK---------pKAYLSTMYIGLDFN----kEKVDIHIPCTEFV` `:` `2o1p(A) : ITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALKLVTDEiKDAPKAYLSTMYIGLDFNIENKKEKVDIHIPCTEFV` `___________________385_389______________________________________________________________________________________________` `____________________________520____________` `2hhp(A) : NLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRPS**` `:` `2o1p(A) : NLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRPSKK` `____________________________520____________`

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)	9.8
Translation (A)	-0.7
Closure (%)	76.8
Bending Residues ( green )	224 - 225 231 - 232 315 - 316 318 - 319 354 - 355 385 - 386 389 - 390 520 - 521 523 - 525
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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