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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	380	0.32	30 - 44 55 - 64 70 - 71 105 - 107 132 - 133 188 - 388 390 - 419 422 - 422 424 - 539
2	130	0.25	45 - 54 65 - 69 72 - 104 108 - 131 134 - 187 389 - 389 420 - 421 423 - 423

Sequence

`_______________________44________54________64__68______________________________101___________________________131________` `6dqr(A) : *******TQLDEKQHIVINNGAEPQSFDPHKTEGVPESNVAYQLLEGLVTSDSEGKLQPGAAESWENTPDFKTWTFHLRKDAKWSNGDPVTAHDFVFAWRRLVDPATAAPYASYLSYLQV` `:` `6dtg(A) : MVIVPEGTQLDEKQHIVINNGAEPQSFDPHKTEGVPESNVAYQLLEGLVTSDSEGKLQPGAAESWENTPDFKTWTFHLRKDAKWSNGDPVTAHDFVFAWRRLVDPATAAPYASYLSYLQV` `_______________________44________54________64__68______________________________101___________________________131________` `_____________________________________________187________________________________________________________________________` `6dqr(A) : ENAQDIIDGKKKPAELGVEAKDDYTFVVHATNPVPYAVSLTTHQSLLPLPQKVVEKLGDAWVKKENYVGNGAYKLANHIINEKIEFERNPLYWNDKETVINSATFLAIENPSTDVARYRA` `:` `6dtg(A) : ENAQDIIDGKKKPAELGVEAKDDYTFVVHATNPVPYAVSLTTHQSLLPLPQKVVEKLGDAWVKKENYVGNGAYKLANHIINEKIEFERNPLYWNDKETVINSATFLAIENPSTDVARYRA` `_____________________________________________187________________________________________________________________________` `________________________________________________________________________________________________________________________` `6dqr(A) : GDLDMTSYGLPPEQFAKLKKELLGEVYVTRTLGTYSYELNNKKAPFDNVNIRKALNLSLDRNVITDKVLGQGQTPTYVFTPTYIEEGHLIQQPAYSKEPMAQRNEEAIKLLEEAGYSKAN` `:` `6dtg(A) : GDLDMTSYGLPPEQFAKLKKELLGEVYVTRTLGTYSYELNNKKAPFDNVNIRKALNLSLDRNVITDKVLGQGQTPTYVFTPTYIEEGHLIQQPAYSKEPMAQRNEEAIKLLEEAGYSKAN` `________________________________________________________________________________________________________________________` `______388____________________________419________________________________________________________________________________` `6dqr(A) : PLKFSILYNTNENHKKVAIAAASMWKANTKGLIDVKLENQEWKTYIDSRRAGRYDVARAGWHADYNQATTFGNYFLSNSSNNTAKYANPEYDKAMAESYAATDAEGRAKAYAKAEEILGK` `:` `6dtg(A) : PLKFSILYNTNENHKKVAIAAASMWKANTKGLIDVKLENQEWKTYIDSRRAGRYDVARAGWHADYNQATTFGNYFLSNSSNNTAKYANPEYDKAMAESYAATDAEGRAKAYAKAEEILGK` `______388____________________________419________________________________________________________________________________` `__________________________________________` `6dqr(A) : DYGIVPIFNYVNPRLVKPYVKGYSGKDPQDHIYLRNLYIIKH` `:` `6dtg(A) : DYGIVPIFNYVNPRLVKPYVKGYSGKDPQDHIYLRNLYIIKH` `__________________________________________`

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)	2.5
Translation (A)	0.1
Closure (%)	19.1
Bending Residues ( green )	44 - 46 54 - 55 64 - 65 68 - 77 101 - 109 131 - 135 187 - 192 388 - 390 419 - 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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