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)	6dqq (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	384	0.31	30 - 45 55 - 65 70 - 75 105 - 106 131 - 133 187 - 189 192 - 388 390 - 419 424 - 539
2	126	0.22	46 - 54 66 - 69 76 - 104 107 - 130 134 - 186 190 - 191 389 - 389 420 - 423

Sequence

`_______________________45_______54_________65_68_____75________________________102_________________________130__________` `6dqr(A) : ******TQLDEKQHIVINNGAEPQSFDPHKTEGVPESNVAYQLLEGLVTSDSEGKLQPGAAESWENTPDFKTWTFHLRKDAKWSNGDPVTAHDFVFAWRRLVDPATAAPYASYLSYLQVE` `:` `6dqq(A) : VIVPEGTQLDEKQHIVINNGAEPQSFDPHKTEGVPESNVAYQLLEGLVTSDSEGKLQPGAAESWENTPDFKTWTFHLRKDAKWSNGDPVTAHDFVFAWRRLVDPATAAPYASYLSYLQVE` `_______________________45_______54_________65_68_____75________________________102_________________________130__________` `___________________________________________186__________________________________________________________________________` `6dqr(A) : NAQDIIDGKKKPAELGVEAKDDYTFVVHATNPVPYAVSLTTHQSLLPLPQKVVEKLGDAWVKKENYVGNGAYKLANHIINEKIEFERNPLYWNDKETVINSATFLAIENPSTDVARYRAG` `:` `6dqq(A) : NAQDIIDGKKKPAELGVEAKDDYTFVVHATNPVPYAVSLTTHQSLLPLPQKVVEKLGDAWVKKENYVGNGAYKLANHIINEKIEFERNPLYWNDKETVINSATFLAIENPSTDVARYRAG` `___________________________________________186__________________________________________________________________________` `________________________________________________________________________________________________________________________` `6dqr(A) : DLDMTSYGLPPEQFAKLKKELLGEVYVTRTLGTYSYELNNKKAPFDNVNIRKALNLSLDRNVITDKVLGQGQTPTYVFTPTYIEEGHLIQQPAYSKEPMAQRNEEAIKLLEEAGYSKANP` `:` `6dqq(A) : DLDMTSYGLPPEQFAKLKKELLGEVYVTRTLGTYSYELNNKKAPFDNVNIRKALNLSLDRNVITDKVLGQGQTPTYVFTPTYIEEGHLIQQPAYSKEPMAQRNEEAIKLLEEAGYSKANP` `________________________________________________________________________________________________________________________` `_____388____________________________419_423_____________________________________________________________________________` `6dqr(A) : LKFSILYNTNENHKKVAIAAASMWKANTKGLIDVKLENQEWKTYIDSRRAGRYDVARAGWHADYNQATTFGNYFLSNSSNNTAKYANPEYDKAMAESYAATDAEGRAKAYAKAEEILGKD` `:` `6dqq(A) : LKFSILYNTNENHKKVAIAAASMWKANTKGLIDVKLENQEWKTYIDSRRAGRYDVARAGWHADYNQATTFGNYFLSNSSNNTAKYANPEYDKAMAESYAATDAEGRAKAYAKAEEILGKD` `_____388____________________________419_423_____________________________________________________________________________` `_________________________________________` `6dqr(A) : YGIVPIFNYVNPRLVKPYVKGYSGKDPQDHIYLRNLYIIKH` `:` `6dqq(A) : YGIVPIFNYVNPRLVKPYVKGYSGKDPQDHIYLRNLYIIKH` `_________________________________________`

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)	2.6
Translation (A)	0.1
Closure (%)	18.8
Bending Residues ( green )	45 - 46 54 - 55 65 - 66 68 - 70 75 - 77 102 - 108 130 - 131 133 - 135 186 - 192 388 - 390 419 - 420 423 - 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

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