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)	3tcf (A)
Conformer 2 (PDB)	3tch (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	292	0.69	29 - 273 278 - 294 335 - 335 513 - 541
2	221	1.12	274 - 277 295 - 334 336 - 512

Sequence

`________________________________________________________________________________________________________________________` `3tcf(A) : ADVPAGVTLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLVSDLDGHPAPGVAESWDNKDAKVWTFHLRKDAKWSDGTPVTAQDFVYSWQRSVDPNTASPYASYLQYGHIAG` `:` `3tch(A) : ADVPAGVTLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLVSDLDGHPAPGVAESWDNKDAKVWTFHLRKDAKWSDGTPVTAQDFVYSWQRSVDPNTASPYASYLQYGHIAG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3tcf(A) : IDEILEGKKPITDLGVKAIDDHTLEVTLSEPVPYFYKLLVHPSTSPVPKAAIEKFGEKWTQPGNIVTNGAYTLKDWVVNERIVLERSPTYWNNAKTVINQVTYLPIASEVTDVNRYRSGE` `:` `3tch(A) : IDEILEGKKPITDLGVKAIDDHTLEVTLSEPVPYFYKLLVHPSTSPVPKAAIEKFGEKWTQPGNIVTNGAYTLKDWVVNERIVLERSPTYWNNAKTVINQVTYLPIASEVTDVNRYRSGE` `________________________________________________________________________________________________________________________` `____273__________________294________________________________329_________________________________________________________` `3tcf(A) : IDMTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGMDRDIIVNKVKAQGNMPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLT` `:` `3tch(A) : IDMTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGMDRDIIVNKVKAQGNMPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLT` `____273__________________294________________________________329_________________________________________________________` `________________________________________________________________________________________________________________________` `3tcf(A) : INLLYNTSDLHKKLAIAASSLWKKNIGVNVKLVNQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSMNTAHYKSPAFDSIMAETLKVTDEAQRTALYTKAEQQLDKDSAIV` `:` `3tch(A) : INLLYNTSDLHKKLAIAASSLWKKNIGVNVKLVNQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSMNTAHYKSPAFDSIMAETLKVTDEAQRTALYTKAEQQLDKDSAIV` `________________________________________________________________________________________________________________________` `__511________________________________` `3tcf(A) : PVYYYVNARLVKPWVGGYTGKDPLDNTYTRNMYIVKH` `:` `3tch(A) : PVYYYVNARLVKPWVGGYTGKDPLDNTYTRNMYIVKH` `__511________________________________`

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)	42.2
Translation (A)	0.9
Closure (%)	85.5
Bending Residues ( green )	273 - 282 294 - 296 329 - 337 511 - 514
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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