DynDom - Protein Domain Motions

Sarcoplasmic/endoplasmic Reticulum Calcium Atpase 1 Isoform 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	Sarcoplasmic/endoplasmic Reticulum Calcium Atpase 1 Isoform Serca1a
Conformer 1 (PDB)	1t5s (A)
Conformer 2 (PDB)	1su4 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	600	4.69	43 - 127 236 - 359 602 - 992
2	148	0.66	3 - 42 128 - 235
3	242	0.92	360 - 601

Sequence

`_______________________________________41_______________________________________________________________________________` `1t5s(A) : MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK` `:` `1su4(A) : MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK` `_______________________________________41_______________________________________________________________________________` `____127_________________________________________________________________________________________________________235_____` `1t5s(A) : EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA` `:` `1su4(A) : EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA` `____127_________________________________________________________________________________________________________235_____` `____________________________________________________________________________________________________________________359_` `1t5s(A) : ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ` `:` `1su4(A) : ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ` `____________________________________________________________________________________________________________________359_` `________________________________________________________________________________________________________________________` `1t5s(A) : MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK` `:` `1su4(A) : MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________________________________________599_` `1t5s(A) : KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML` `:` `1su4(A) : KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML` `____________________________________________________________________________________________________________________599_` `________________________________________________________________________________________________________________________` `1t5s(A) : DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM` `:` `1su4(A) : DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1t5s(A) : GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI` `:` `1su4(A) : GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1t5s(A) : GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK` `:` `1su4(A) : GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK` `________________________________________________________________________________________________________________________` `__________________________________` `1t5s(A) : ALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG` `:` `1su4(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)	44.8
Translation (A)	0.2
Closure (%)	72.9
Bending Residues ( green )	41 - 43 127 - 128 235 - 236
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	83.9
Translation (A)	7.0
Closure (%)	99.7
Bending Residues ( green )	359 - 362 599 - 602
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

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