DynDom - Protein Domain Motions

Preprotein Translocase Seca Subunit

(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	Preprotein Translocase Seca Subunit
Conformer 1 (PDB)	2ipc (A)
Conformer 2 (PDB)	2ipc (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	520	0.64	13 - 222 371 - 467 542 - 754
2	331	0.7	223 - 370 755 - 937
3	74	0.11	468 - 541

Sequence

`________________________________________________________________________________________________________________________` `2ipc(A) : MLGLLRRLFDNNEREIARYYKQVVEPVNRLEAEVEKLPDLAAAYRELKEKHEKGASLDELLPMAFALTRESAKRYLGMRHFDVQLIGGAVLHEGKIAEMKTGEGKTLVATLAVALNALTG` `:` `2ipc(B) : *****RRLFDNNEREIARYYKQVVEPVNRLEAEVEKLPDLAAAYRELKEKHEKGASLDELLPMAFALTRESAKRYLGMRHFDVQLIGGAVLHEGKIAEMKTGEGKTLVATLAVALNALTG` `________________________________________________________________________________________________________________________` `__________________________________________________________________________________________________221___________________` `2ipc(A) : KGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEARTPLIISGPAEKATDLYYKMA` `:` `2ipc(B) : KGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEARTPLIISGPAEKATDLYYKMA` `__________________________________________________________________________________________________221___________________` `________________________________________________________________________________________________________________________` `2ipc(A) : EIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELAHMLIQAIRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIE` `:` `2ipc(B) : EIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELAHMLIQAIRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIE` `________________________________________________________________________________________________________________________` `______369___________________________________________________________________________________________463_________________` `2ipc(A) : RENQTLATITYQNFFRLYEKRAGMTGTAKTEEKEFQEIYGMDVVVVPTNRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLKEPRLYLPRLEMRLELF` `:` `2ipc(B) : RENQTLATITYQNFFRLYEKRAGMTGTAKTEEKEFQEIYGMDVVVVPTNRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLKEPRLYLPRLEMRLELF` `______369___________________________________________________________________________________________463_________________` `__________________________________________________________541___________________________________________________________` `2ipc(A) : KKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGIPHQVLNAKHHAREAEIVAQAGRSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKE` `:` `2ipc(B) : KKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGIPHQVLNAKHHAREAEIVAQAGRSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKE` `__________________________________________________________541___________________________________________________________` `________________________________________________________________________________________________________________________` `2ipc(A) : GFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDDLMRLFASDRVIAMLDRMGFD` `:` `2ipc(B) : GFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDDLMRLFASDRVIAMLDRMGFD` `________________________________________________________________________________________________________________________` `______________________________753_______________________________________________________________________________________` `2ipc(A) : DSEPIEHPMVTRSIERAQKRVEDRNFAIRKQLLQFDDVLSRQREVIYAQRRLILLGKDEEVKEAAIGMVEETVASLAENFLNPEVHPEDWDLEGLKATLLDTAPQLQDFPFAELRALKAE` `:` `2ipc(B) : DSEPIEHPMVTRSIERAQKRVEDRNFAIRKQLLQFDDVLSRQREVIYAQRRLILLGKDEEVKEAAIGMVEETVASLAENFLNPEVHPEDWDLEGLKATLLDTAPQLQDFPFAELRALKAE` `______________________________753_______________________________________________________________________________________` `___________________________________________________________________________________________________` `2ipc(A) : EAVERLVEAALKAYEAREAELSPPLMRAVERFVILNVVDNAWKEHLHNLDVLRQGIFLRGYGQKDPFQEYKIEATRLFNEMVAFIKSEVAKFLFRLKVE` `:` `2ipc(B) : EAVERLVEAALKAYEAREAELSPPLMRAVERFVILNVVDNAWKEHLHNLDVLRQGIFLRGYGQKDPFQEYKIEATRLFNEMVAFIKSEVAKFLFRLKVE` `___________________________________________________________________________________________________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	5.5
Translation (A)	-0.4
Closure (%)	88.7
Bending Residues ( green )	221 - 223 369 - 371 753 - 756
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	7.2
Translation (A)	0.3
Closure (%)	98.8
Bending Residues ( green )	463 - 473 541 - 544
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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

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

Movement classification: Hinge

PyMOL Script

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