DynDom - Protein Domain Motions

Protein Translocase Subunit Seca

(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	Protein Translocase Subunit Seca
Conformer 1 (PDB)	4ys0 (A)
Conformer 2 (PDB)	3jux (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	503	0.9	6 - 231 241 - 267 400 - 640 644 - 650 787 - 788
2	302	1.19	232 - 240 268 - 399 641 - 643 651 - 786 789 - 814

Sequence

`________________________________________________________________________________________________________________________` `4ys0(A) : ILFDKNKRILKKYAKMVSKINQIESDLRSKKNSELIRLSMVLKEKVNSFEDADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTLAATMPIYLNALIGKGVHL` `:` `3jux(A) : FDKNKRILKKYAKMVSKINQIESDLRSKKNSELIRLSMVLKEKVNSFEDADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTLAATMPIYLNALIGKGVHL` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________________231______240_` `4ys0(A) : VTVNDYLARRDALWMGPVYLFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDK` `:` `3jux(A) : VTVNDYLARRDALWMGPVYLFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDK` `___________________________________________________________________________________________________________231______240_` `_______________________267______________________________________________________________________________________________` `4ys0(A) : VQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIV` `:` `3jux(A) : VQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIV` `_______________________267______________________________________________________________________________________________` `___________________________________399__________________________________________________________________________________` `4ys0(A) : DEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGT` `:` `3jux(A) : DEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGT` `___________________________________399__________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4ys0(A) : TSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGK` `:` `3jux(A) : TSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGK` `________________________________________________________________________________________________________________________` `____________________________________640_______650_______________________________________________________________________` `4ys0(A) : VMNILKIEEGQPIQHPMLSKLIENIQKKVEGINFSIRKTLMEMDDVLDKQRRAVYSLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKNSLSFFPAGLFDLDEKQFSSSE` `:` `3jux(A) : VMNILKIEEGQPIQHPMLSKLIENIQKKVEGINFSIRKTLMEMDDVLDKQRRAVYSLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKNSLSFFPAGLFDLDEKQFSSSE` `____________________________________640_______650_______________________________________________________________________` `______________________________________________________________786_________________________________` `4ys0(A) : ELHDYLFNRLWEEYQRKKQEIGEDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRS----dPIVEFKKETYYMFDEMMRRINDTIANYVLRVLEH` `:` `3jux(A) : ELHDYLFNRLWEEYQRKKQEIGEDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV*` `______________________________________________________________786_________________________________`

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)	11.5
Translation (A)	0.7
Closure (%)	98.6
Bending Residues ( green )	231 - 232 240 - 241 267 - 268 399 - 400 640 - 641 643 - 644 650 - 651 786 - 789
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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