DynDom - Protein Domain Motions

Periplasmic Oligo-Peptide 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 Oligo-Peptide Binding Protein
Conformer 1 (PDB)	1b6h (A)
Conformer 2 (PDB)	1rkm (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	291	0.54	3 - 248 254 - 269 487 - 515
2	222	0.69	249 - 253 270 - 486

Sequence

`________________________________________________________________________________________________________________________` `1b6h(A) : ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIAN` `:` `1rkm(A) : ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIAN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1b6h(A) : IDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE` `:` `1rkm(A) : IDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGE` `________________________________________________________________________________________________________________________` `___246____________________269___________________________________________________________________________________________` `1b6h(A) : IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLT` `:` `1rkm(A) : IDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLT` `___246____________________269___________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1b6h(A) : FDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV` `:` `1rkm(A) : FDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIV` `________________________________________________________________________________________________________________________` `___486_______________________________` `1b6h(A) : PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH` `:` `1rkm(A) : PVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH` `___486_______________________________`

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)	25.9
Translation (A)	0.1
Closure (%)	95.3
Bending Residues ( green )	246 - 255 269 - 271 486 - 488
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

Download and extract PyMOL PML script file

Download