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)	4jsd (A)
Window Length	11
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	362	0.32	7 - 260 431 - 438 449 - 463 465 - 465 471 - 489 511 - 575
2	207	0.26	261 - 430 439 - 448 464 - 464 466 - 470 490 - 510

Sequence

`________________________________________________________________________________________________________________________` `2o7i(A) : SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVV` `:` `4jsd(A) : SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2o7i(A) : EFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWEL` `:` `4jsd(A) : EFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWEL` `________________________________________________________________________________________________________________________` `________________260_____________________________________________________________________________________________________` `2o7i(A) : WEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGV` `:` `4jsd(A) : WEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGV` `________________259_____________________________________________________________________________________________________` `__________________________________________________________________430_____438_______448____________463__________________` `2o7i(A) : RVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLD` `:` `4jsd(A) : RVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLD` `__________________________________________________________________429_____437_______447____________462__________________` `_____489__________________510_________________________________________________________________________` `2o7i(A) : PEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT` `:` `4jsd(A) : PEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT` `_____488__________________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)	2.9
Translation (A)	-0.1
Closure (%)	86.9
Bending Residues ( green )	260 - 261 430 - 431 438 - 439 448 - 449 463 - 471 489 - 490 510 - 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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