DynDom - Protein Domain Motions

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	Periplasmic Oligopeptide-Binding Protein
Conformer 1 (PDB)	6dqr (A)
Conformer 2 (PDB)	6dqt (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	380	0.27	31 - 44 55 - 63 70 - 75 131 - 131 186 - 420 424 - 538
2	128	0.21	45 - 54 64 - 69 76 - 130 132 - 185 421 - 423

Sequence

`______________________44________54_______63___68_____75____________________________________________________130__________` `6dqr(A) : ******TQLDEKQHIVINNGAEPQSFDPHKTEGVPESNVAYQLLEGLVTSDSEGKLQPGAAESWENTPDFKTWTFHLRKDAKWSNGDPVTAHDFVFAWRRLVDPATAAPYASYLSYLQVE` `:` `6dqt(A) : VIVPEGTQLDEKQHIVINNGAEPQSFDPHKTEGVPESNVAYQLLEGLVTSDSEGKLQPGAAESWENTPDFKTWTFHLRKDAKWSNGDPVTAHDFVFAWRRLVDPATAAPYASYLSYLQVE` `______________________44________54_______63___68_____75____________________________________________________130__________` `__________________________________________185___________________________________________________________________________` `6dqr(A) : NAQDIIDGKKKPAELGVEAKDDYTFVVHATNPVPYAVSLTTHQSLLPLPQKVVEKLGDAWVKKENYVGNGAYKLANHIINEKIEFERNPLYWNDKETVINSATFLAIENPSTDVARYRAG` `:` `6dqt(A) : NAQDIIDGKKKPAELGVEAKDDYTFVVHATNPVPYAVSLTTHQSLLPLPQKVVEKLGDAWVKKENYVGNGAYKLANHIINEKIEFERNPLYWNDKETVINSATFLAIENPSTDVARYRAG` `__________________________________________185___________________________________________________________________________` `________________________________________________________________________________________________________________________` `6dqr(A) : DLDMTSYGLPPEQFAKLKKELLGEVYVTRTLGTYSYELNNKKAPFDNVNIRKALNLSLDRNVITDKVLGQGQTPTYVFTPTYIEEGHLIQQPAYSKEPMAQRNEEAIKLLEEAGYSKANP` `:` `6dqt(A) : DLDMTSYGLPPEQFAKLKKELLGEVYVTRTLGTYSYELNNKKAPFDNVNIRKALNLSLDRNVITDKVLGQGQTPTYVFTPTYIEEGHLIQQPAYSKEPMAQRNEEAIKLLEEAGYSKANP` `________________________________________________________________________________________________________________________` `_____________________________________420________________________________________________________________________________` `6dqr(A) : LKFSILYNTNENHKKVAIAAASMWKANTKGLIDVKLENQEWKTYIDSRRAGRYDVARAGWHADYNQATTFGNYFLSNSSNNTAKYANPEYDKAMAESYAATDAEGRAKAYAKAEEILGKD` `:` `6dqt(A) : LKFSILYNTNENHKKVAIAAASMWKANTKGLIDVKLENQEWKTYIDSRRAGRYDVARAGWHADYNQATTFGNYFLSNSSNNTAKYANPEYDKAMAESYAATDAEGRAKAYAKAEEILGKD` `_____________________________________420________________________________________________________________________________` `_________________________________________` `6dqr(A) : YGIVPIFNYVNPRLVKPYVKGYSGKDPQDHIYLRNLYIIKH` `:` `6dqt(A) : YGIVPIFNYVNPRLVKPYVKGYSGKDPQDHIYLRNLYIIKH` `_________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	2.2
Translation (A)	0.0
Closure (%)	22.7
Bending Residues ( green )	44 - 45 54 - 55 63 - 64 68 - 70 75 - 77 130 - 132 185 - 186 420 - 421 423 - 424
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

Download and extract PyMOL PML script file

Download