DynDom - Protein Domain Motions

Serca1a

(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	Serca1a
Conformer 1 (PDB)	3w5a (A)
Conformer 2 (PDB)	3ar2 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	493	3.57	47 - 124 246 - 339 346 - 347 356 - 356 602 - 606 636 - 641 644 - 646 674 - 676 681 - 681 692 - 816 818 - 992
2	158	0.98	3 - 46 125 - 238
3	332	1.86	340 - 345 348 - 355 357 - 601 607 - 635 642 - 643 647 - 673 677 - 680 682 - 691 817 - 817

Sequence

`____________________________________________46______________________________________________________________________119_` `3w5a(A) : MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK` `:` `3ar2(A) : MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK` `____________________________________________46______________________________________________________________________119_` `__________________________________________________________________________________________________________________237___` `3w5a(A) : EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA` `:` `3ar2(A) : EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA` `__________________________________________________________________________________________________________________237___` `________________________________________________________________________________________________339___345_______355_____` `3w5a(A) : ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ` `:` `3ar2(A) : ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ` `________________________________________________________________________________________________339___345_______355_____` `________________________________________________________________________________________________________________________` `3w5a(A) : MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK` `:` `3ar2(A) : MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________________________________60` `3w5a(A) : KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML` `:` `3ar2(A) : KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML` `______________________________________________________________________________________________________________________60` `1__606__________________________635___641__646________________________673____680________691_____________________________` `3w5a(A) : DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM` `:` `3ar2(A) : DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM` `1__606__________________________635___641__646________________________673____680________691_____________________________` `_____________________________________________________________________________________________816________________________` `3w5a(A) : GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI` `:` `3ar2(A) : GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI` `_____________________________________________________________________________________________816________________________` `________________________________________________________________________________________________________________________` `3w5a(A) : GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK` `:` `3ar2(A) : GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK` `________________________________________________________________________________________________________________________` `__________________________________` `3w5a(A) : ALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG` `:` `3ar2(A) : ALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG` `__________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	19.5
Translation (A)	0.0
Closure (%)	60.9
Bending Residues ( green )	46 - 58 119 - 125 237 - 246
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	17.2
Translation (A)	1.3
Closure (%)	89.1
Bending Residues ( green )	339 - 343 345 - 348 355 - 357 601 - 602 606 - 607 635 - 636 641 - 644 646 - 647 673 - 674 676 - 677 680 - 682 691 - 692 816 - 818
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Mixed

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

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

Movement classification: Shear

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