DynDom - Protein Domain Motions

Sarcoplasmic/endoplasmic Reticulum Calcium Atpase 1

(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
Conformer 1 (PDB)	5a3r (A)
Conformer 2 (PDB)	2zbd (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	158	4.83	46 - 121 245 - 312 788 - 801
2	161	1.2	3 - 45 122 - 239
3	422	3.08	313 - 358 602 - 787 802 - 992
4	239	0.78	362 - 600

Sequence

`_________________________________________43___________________________________________________________________________12` `5a3r(A) : MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK` `:` `2zbd(A) : MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK` `_________________________________________43___________________________________________________________________________12` `1_______________________________________________________________________________________________________________235_____` `5a3r(A) : EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA` `:` `2zbd(A) : EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA` `1_______________________________________________________________________________________________________________235_____` `_____________________________________________________________________312___________________________________________358__` `5a3r(A) : ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICS-kTGTLTTNQ` `:` `2zbd(A) : ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ` `_____________________________________________________________________312___________________________________________358__` `________________________________________________________________________________________________________________________` `5a3r(A) : MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK` `:` `2zbd(A) : MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________________________________________599_` `5a3r(A) : KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML` `:` `2zbd(A) : KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML` `____________________________________________________________________________________________________________________599_` `________________________________________________________________________________________________________________________` `5a3r(A) : DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM` `:` `2zbd(A) : DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM` `________________________________________________________________________________________________________________________` `________________________________________________________________787___________801_______________________________________` `5a3r(A) : GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI` `:` `2zbd(A) : GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI` `________________________________________________________________787___________801_______________________________________` `________________________________________________________________________________________________________________________` `5a3r(A) : GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK` `:` `2zbd(A) : GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK` `________________________________________________________________________________________________________________________` `__________________________________` `5a3r(A) : ALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG` `:` `2zbd(A) : ALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG` `__________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	69.1	-3.4	10.9	43 - 46 121 - 126 235 - 245	Bending Region Analysis
1	3	27.7	-1.9	75.6	312 - 313 787 - 788 801 - 802	Bending Region Analysis
3	4	58.7	-1.1	99.6	358 - 362 599 - 602	Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 3 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 3

Movement classification:

No Contacts

PyMOL Script

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