DynDom - Protein Domain Motions

Oligopeptide Abc Transporter, Periplasmic Oligopeptide- Binding Protein

(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	Oligopeptide Abc Transporter, Periplasmic Oligopeptide- Binding Protein
Conformer 1 (PDB)	2o7i (A)
Conformer 2 (PDB)	4jso (A)
Window Length	15
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	332	0.27	9 - 133 135 - 259 468 - 478 486 - 490 511 - 576
2	236	0.28	134 - 134 260 - 467 479 - 485 491 - 510

Sequence

`________________________________________________________________________________________________________________________` `2o7i(A) : SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVV` `:` `4jso(A) : SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVV` `________________________________________________________________________________________________________________________` `_________133____________________________________________________________________________________________________________` `2o7i(A) : EFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWEL` `:` `4jso(A) : EFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWEL` `_________132____________________________________________________________________________________________________________` `_______________259______________________________________________________________________________________________________` `2o7i(A) : WEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGV` `:` `4jso(A) : WEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGV` `_______________258______________________________________________________________________________________________________` `______________________________________________________________________________________________________466_________478___` `2o7i(A) : RVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLD` `:` `4jso(A) : RVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLD` `______________________________________________________________________________________________________465_________477___` `_485__490_________________510_________________________________________________________________________` `2o7i(A) : PEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT` `:` `4jso(A) : PEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT` `_484__489_________________509_________________________________________________________________________`

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)	2.1
Translation (A)	-0.1
Closure (%)	82.7
Bending Residues ( green )	133 - 135 259 - 263 466 - 468 478 - 479 485 - 486 490 - 492 510 - 511
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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